Starting phenix.real_space_refine
on Tue Mar  3 16:34:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2026/6vk1_21223.cif"
  }
  resolution = 3.9
  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=   0.008
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      34      5.16       5
     C    4712      2.51       5
     N    1203      2.21       5
     O    1310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 7259
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2343
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 4916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4916
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 20, 'TRANS': 581}
          Chain breaks: 5
  Time building chain proxies: 1.67, per 1000 atoms: 0.23
  Number of scatterers: 7259
  At special positions: 0
  Unit cell: (78.3, 99.9, 152.55, 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      34     16.00
     O    1310      8.00
     N    1203      7.00
     C    4712      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: 0.69
  Conformation dependent library (CDL) restraints added in 251.8 milliseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1700

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      79.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 31
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 44 through 71
    Processing helix  chain 'B' and resid 75 through 98
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 99 through 100
      No H-bonds generated for 'chain 'B' and resid 99 through 100'
    Processing helix  chain 'B' and resid 101 through 104
    Processing helix  chain 'B' and resid 105 through 135
      removed outlier: 3.856A  pdb=" N   ALA B 109 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 175
    Processing helix  chain 'B' and resid 179 through 220
      removed outlier: 3.560A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 4.022A  pdb=" N   TYR B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 297 through 324
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
      removed outlier: 3.583A  pdb=" N   PHE A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
      removed outlier: 3.877A  pdb=" N   THR A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 138
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.676A  pdb=" N   ILE A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.604A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
      removed outlier: 3.601A  pdb=" N   LYS A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY A 200 " --> pdb=" O   LYS A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 224
      removed outlier: 4.131A  pdb=" N   SER A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
      removed outlier: 3.630A  pdb=" N   TRP A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 329
      removed outlier: 4.318A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 3.932A  pdb=" N   ALA A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 361
      removed outlier: 5.558A  pdb=" N   ASP A 359 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 360 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 4.058A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.931A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
      removed outlier: 3.869A  pdb=" N   TYR A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.995A  pdb=" N   ALA A 433 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 4.080A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 465'
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.708A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 3.767A  pdb=" N   THR A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.911A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 548
      removed outlier: 4.023A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.805A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 609
      removed outlier: 3.683A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
      removed outlier: 3.662A  pdb=" N   LEU A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.686A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 682

    498 hydrogen bonds defined for protein.
    1488 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2267
        1.34 -     1.46: 1464
        1.46 -     1.58: 3645
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7437
  Sorted by residual:
  bond pdb=" N   HIS B 101 "
       pdb=" CA  HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.91e+00
  bond pdb=" N   GLU B 102 "
       pdb=" CA  GLU B 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.031 1.27e-02 6.20e+03 6.07e+00
  bond pdb=" N   ARG B 103 "
       pdb=" CA  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.028 1.16e-02 7.43e+03 5.72e+00
  bond pdb=" CE1 HIS B 101 "
       pdb=" NE2 HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 3.03e+00
  bond pdb=" CA  HIS B 101 "
       pdb=" C   HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.015 1.34e-02 5.57e+03 1.30e+00
  ... (remaining 7432 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 9622
        1.28 -     2.57: 370
        2.57 -     3.85: 56
        3.85 -     5.14: 13
        5.14 -     6.42: 4
  Bond angle restraints: 10065
  Sorted by residual:
  angle pdb=" N   GLY A 253 "
        pdb=" CA  GLY A 253 "
        pdb=" C   GLY A 253 "
      ideal   model   delta    sigma   weight residual
     112.48  118.47   -5.99 1.21e+00 6.83e-01 2.45e+01
  angle pdb=" C   ASN A 533 "
        pdb=" N   ASP A 534 "
        pdb=" CA  ASP A 534 "
      ideal   model   delta    sigma   weight residual
     121.54  127.96   -6.42 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" C   PHE A 201 "
        pdb=" N   ASN A 202 "
        pdb=" CA  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     121.54  127.39   -5.85 1.91e+00 2.74e-01 9.38e+00
  angle pdb=" CA  ARG B 103 "
        pdb=" C   ARG B 103 "
        pdb=" O   ARG B 103 "
      ideal   model   delta    sigma   weight residual
     121.07  117.91    3.16 1.10e+00 8.26e-01 8.26e+00
  angle pdb=" C   PHE B 214 "
        pdb=" N   TYR B 215 "
        pdb=" CA  TYR B 215 "
      ideal   model   delta    sigma   weight residual
     120.79  124.54   -3.75 1.39e+00 5.18e-01 7.29e+00
  ... (remaining 10060 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 3880
       17.65 -    35.31: 440
       35.31 -    52.96: 64
       52.96 -    70.61: 14
       70.61 -    88.26: 5
  Dihedral angle restraints: 4403
    sinusoidal: 1772
      harmonic: 2631
  Sorted by residual:
  dihedral pdb=" CA  ASN A 645 "
           pdb=" C   ASN A 645 "
           pdb=" N   ARG A 646 "
           pdb=" CA  ARG A 646 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.61   22.39     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  ALA A  38 "
           pdb=" C   ALA A  38 "
           pdb=" N   LYS A  39 "
           pdb=" CA  LYS A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.05  -19.95     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  SER A 245 "
           pdb=" C   SER A 245 "
           pdb=" N   ASP A 246 "
           pdb=" CA  ASP A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 4400 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 784
       0.037 -    0.075: 265
       0.075 -    0.112: 46
       0.112 -    0.149: 10
       0.149 -    0.187: 1
  Chirality restraints: 1106
  Sorted by residual:
  chirality pdb=" CA  LEU A 252 "
            pdb=" N   LEU A 252 "
            pdb=" C   LEU A 252 "
            pdb=" CB  LEU A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CB  VAL B 155 "
            pdb=" CA  VAL B 155 "
            pdb=" CG1 VAL B 155 "
            pdb=" CG2 VAL B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  VAL A 203 "
            pdb=" N   VAL A 203 "
            pdb=" C   VAL A 203 "
            pdb=" CB  VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1103 not shown)

  Planarity restraints: 1257
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 295 "   -0.029 5.00e-02 4.00e+02   4.33e-02 3.01e+00
        pdb=" N   PRO B 296 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B   2 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO B   3 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B   3 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B   3 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 102 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   GLU B 102 "    0.027 2.00e-02 2.50e+03
        pdb=" O   GLU B 102 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ARG B 103 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1254 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1500
        2.78 -     3.31: 7437
        3.31 -     3.84: 11683
        3.84 -     4.37: 12815
        4.37 -     4.90: 21844
  Nonbonded interactions: 55279
  Sorted by model distance:
  nonbonded pdb=" O   THR B 144 "
            pdb=" OG  SER B 148 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" CD1 LEU B 285 "
            pdb=" ND1 HIS B 286 "
     model   vdw
     2.250 3.540
  nonbonded pdb=" O   ASP B 179 "
            pdb=" OG  SER B 182 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" OE1 GLN A 453 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OH  TYR B 104 "
            pdb=" OD2 ASP B 179 "
     model   vdw
     2.296 3.040
  ... (remaining 55274 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.060
  Find NCS groups from input model:        0.030
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.003   0.036   7437  Z= 0.151
  Angle     :  0.590   6.422  10065  Z= 0.362
  Chirality :  0.038   0.187   1106
  Planarity :  0.004   0.043   1257
  Dihedral  : 14.769  88.262   2703
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.80 %
  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: -1.86 (0.25), residues: 866
  helix: -0.46 (0.18), residues: 659
  sheet:  None (None), residues: 0
  loop : -3.52 (0.32), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 265 
 TYR   0.011   0.001   TYR A  74 
 PHE   0.013   0.001   PHE B 147 
 TRP   0.016   0.001   TRP A  27 
 HIS   0.004   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7437)
  covalent geometry    : angle       0.59001 (10065)
  hydrogen bonds       : bond        0.09755 (  498)
  hydrogen bonds       : angle       4.90803 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8411 (mt0) cc_final: 0.8098 (tm-30)
REVERT: B   60 THR cc_start: 0.9238 (p) cc_final: 0.8945 (p)
REVERT: B   85 ARG cc_start: 0.8645 (mmt180) cc_final: 0.7813 (mmm160)
REVERT: B  103 ARG cc_start: 0.5868 (mpp80) cc_final: 0.4331 (ptm-80)
REVERT: B  118 LEU cc_start: 0.8831 (mt) cc_final: 0.8257 (mt)
REVERT: B  122 HIS cc_start: 0.8242 (m90) cc_final: 0.8004 (m170)
REVERT: B  124 ILE cc_start: 0.9062 (pt) cc_final: 0.8737 (pt)
REVERT: B  197 LEU cc_start: 0.9220 (tp) cc_final: 0.8927 (tp)
REVERT: B  202 ASN cc_start: 0.7890 (t0) cc_final: 0.7326 (t0)
REVERT: B  206 GLN cc_start: 0.7832 (mt0) cc_final: 0.7281 (mt0)
REVERT: A  149 LEU cc_start: 0.9375 (tp) cc_final: 0.9067 (mm)
REVERT: A  238 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: A  416 CYS cc_start: 0.8271 (m) cc_final: 0.8052 (m)
REVERT: A  639 GLU cc_start: 0.8037 (pp20) cc_final: 0.7656 (pt0)
REVERT: A  642 LEU cc_start: 0.6235 (pp) cc_final: 0.5212 (pp)
REVERT: A  676 LEU cc_start: 0.7656 (tp) cc_final: 0.7311 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0877
  time to fit residues: 27.3952
Evaluate side-chains
  168 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 189 GLN
A  86 GLN
A 101 ASN
A 113 HIS
A 202 ASN
A 593 GLN
A 620 GLN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.151693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120116 restraints weight = 12674.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.119971 restraints weight = 13788.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.120896 restraints weight = 12858.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122661 restraints weight = 8735.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122818 restraints weight = 7194.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7437  Z= 0.211
  Angle     :  0.662  13.503  10065  Z= 0.348
  Chirality :  0.042   0.182   1106
  Planarity :  0.004   0.045   1257
  Dihedral  :  4.694  24.026    973
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.36 %
    Favored  : 81.98 %
  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: -0.10 (0.27), residues: 866
  helix:  0.85 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.13 (0.34), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.018   0.002   TYR A 486 
 PHE   0.021   0.002   PHE A 367 
 TRP   0.009   0.001   TRP A 632 
 HIS   0.008   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 7437)
  covalent geometry    : angle       0.66243 (10065)
  hydrogen bonds       : bond        0.05130 (  498)
  hydrogen bonds       : angle       4.29930 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8611 (mt0) cc_final: 0.8231 (tm-30)
REVERT: B   60 THR cc_start: 0.9257 (p) cc_final: 0.9007 (p)
REVERT: B   83 PHE cc_start: 0.6541 (t80) cc_final: 0.6304 (t80)
REVERT: B   85 ARG cc_start: 0.8802 (mmt180) cc_final: 0.7733 (mmm160)
REVERT: B  103 ARG cc_start: 0.6057 (mpp80) cc_final: 0.3669 (ttp-170)
REVERT: B  118 LEU cc_start: 0.8845 (mt) cc_final: 0.8603 (mm)
REVERT: B  187 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7596 (tt)
REVERT: B  197 LEU cc_start: 0.9314 (tp) cc_final: 0.8875 (tp)
REVERT: B  298 MET cc_start: 0.8206 (mtt) cc_final: 0.7568 (mpp)
REVERT: A   74 TYR cc_start: 0.7456 (t80) cc_final: 0.7145 (t80)
REVERT: A   78 TRP cc_start: 0.9013 (t-100) cc_final: 0.8801 (t-100)
REVERT: A  113 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8124 (m90)
REVERT: A  149 LEU cc_start: 0.9349 (tp) cc_final: 0.9097 (mm)
REVERT: A  341 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7249 (mm-30)
REVERT: A  344 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8466 (ttpp)
REVERT: A  416 CYS cc_start: 0.8397 (m) cc_final: 0.8032 (m)
REVERT: A  423 ASN cc_start: 0.8444 (p0) cc_final: 0.8225 (p0)
REVERT: A  656 ASP cc_start: 0.7598 (m-30) cc_final: 0.7358 (m-30)
  outliers start: 21
  outliers final: 9
  residues processed: 181
  average time/residue: 0.0728
  time to fit residues: 18.0243
Evaluate side-chains
  168 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  147 PHE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  658 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.154940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124078 restraints weight = 12613.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122342 restraints weight = 10242.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123277 restraints weight = 10654.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.124249 restraints weight = 7481.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.124828 restraints weight = 6412.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7437  Z= 0.125
  Angle     :  0.599  12.359  10065  Z= 0.305
  Chirality :  0.038   0.136   1106
  Planarity :  0.004   0.051   1257
  Dihedral  :  4.347  20.365    973
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.02 %
    Favored  : 79.82 %
  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:  0.90 (0.28), residues: 866
  helix:  1.58 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.70 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 128 
 TYR   0.021   0.001   TYR A 368 
 PHE   0.026   0.001   PHE B 293 
 TRP   0.007   0.001   TRP A 632 
 HIS   0.006   0.001   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7437)
  covalent geometry    : angle       0.59879 (10065)
  hydrogen bonds       : bond        0.04361 (  498)
  hydrogen bonds       : angle       3.87090 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8586 (mt0) cc_final: 0.8113 (tm-30)
REVERT: B   60 THR cc_start: 0.9079 (p) cc_final: 0.8846 (p)
REVERT: B   83 PHE cc_start: 0.6866 (t80) cc_final: 0.6595 (t80)
REVERT: B   85 ARG cc_start: 0.8810 (mmt180) cc_final: 0.7734 (mmm160)
REVERT: B  103 ARG cc_start: 0.5875 (mpp80) cc_final: 0.3712 (ttp-170)
REVERT: B  142 MET cc_start: 0.4937 (tpt) cc_final: 0.4659 (tpt)
REVERT: B  195 MET cc_start: 0.7988 (mtp) cc_final: 0.7783 (mtp)
REVERT: B  197 LEU cc_start: 0.9364 (tp) cc_final: 0.8944 (tp)
REVERT: A  152 MET cc_start: 0.8858 (tpp) cc_final: 0.8372 (tpp)
REVERT: A  248 GLU cc_start: 0.7584 (mp0) cc_final: 0.7116 (mp0)
REVERT: A  344 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8432 (ptmm)
REVERT: A  374 GLN cc_start: 0.8588 (mt0) cc_final: 0.8332 (mm110)
REVERT: A  416 CYS cc_start: 0.8444 (m) cc_final: 0.8103 (m)
REVERT: A  423 ASN cc_start: 0.8406 (p0) cc_final: 0.8167 (p0)
REVERT: A  656 ASP cc_start: 0.7497 (m-30) cc_final: 0.7243 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 182
  average time/residue: 0.0721
  time to fit residues: 18.3064
Evaluate side-chains
  164 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
** B 286 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 = 0.3814 r_free = 0.3814 target = 0.153950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.121782 restraints weight = 12864.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.119547 restraints weight = 12584.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120444 restraints weight = 10078.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121169 restraints weight = 7851.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121339 restraints weight = 7792.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7437  Z= 0.146
  Angle     :  0.617  11.402  10065  Z= 0.312
  Chirality :  0.039   0.224   1106
  Planarity :  0.004   0.045   1257
  Dihedral  :  4.330  27.352    973
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.29 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.28), residues: 866
  helix:  1.69 (0.19), residues: 657
  sheet:  None (None), residues: 0
  loop : -2.60 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.012   0.001   TYR A  90 
 PHE   0.030   0.002   PHE B 277 
 TRP   0.006   0.001   TRP A 541 
 HIS   0.003   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7437)
  covalent geometry    : angle       0.61663 (10065)
  hydrogen bonds       : bond        0.04455 (  498)
  hydrogen bonds       : angle       3.94139 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8627 (mt0) cc_final: 0.8096 (tm-30)
REVERT: B   60 THR cc_start: 0.9092 (p) cc_final: 0.8859 (p)
REVERT: B   83 PHE cc_start: 0.6968 (t80) cc_final: 0.6678 (t80)
REVERT: B   85 ARG cc_start: 0.8885 (mmt180) cc_final: 0.7800 (mmm160)
REVERT: B  192 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7875 (mm-30)
REVERT: B  195 MET cc_start: 0.8060 (mtp) cc_final: 0.7737 (mtp)
REVERT: B  197 LEU cc_start: 0.9376 (tp) cc_final: 0.8955 (tp)
REVERT: A   74 TYR cc_start: 0.7612 (t80) cc_final: 0.7288 (t80)
REVERT: A  344 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8453 (ptmm)
REVERT: A  374 GLN cc_start: 0.8600 (mt0) cc_final: 0.8324 (mm110)
REVERT: A  416 CYS cc_start: 0.8441 (m) cc_final: 0.8078 (m)
REVERT: A  423 ASN cc_start: 0.8382 (p0) cc_final: 0.8113 (p0)
REVERT: A  624 LEU cc_start: 0.8890 (mp) cc_final: 0.8633 (mt)
REVERT: A  656 ASP cc_start: 0.7649 (m-30) cc_final: 0.7412 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 182
  average time/residue: 0.0636
  time to fit residues: 16.5556
Evaluate side-chains
  168 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 286 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.155118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124469 restraints weight = 12803.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124114 restraints weight = 10277.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124910 restraints weight = 10189.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126045 restraints weight = 7272.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.126386 restraints weight = 6333.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7437  Z= 0.126
  Angle     :  0.620  11.027  10065  Z= 0.311
  Chirality :  0.039   0.296   1106
  Planarity :  0.004   0.062   1257
  Dihedral  :  4.228  25.939    973
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.69 %
    Favored  : 76.52 %
  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:  1.36 (0.28), residues: 866
  helix:  1.89 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.45 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.013   0.001   TYR A 436 
 PHE   0.031   0.001   PHE B 293 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.002   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7437)
  covalent geometry    : angle       0.62012 (10065)
  hydrogen bonds       : bond        0.04154 (  498)
  hydrogen bonds       : angle       3.81438 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8480 (mt0) cc_final: 0.8009 (tm-30)
REVERT: B   60 THR cc_start: 0.9028 (p) cc_final: 0.8825 (p)
REVERT: B   83 PHE cc_start: 0.6697 (t80) cc_final: 0.6465 (t80)
REVERT: B   85 ARG cc_start: 0.8679 (mmt180) cc_final: 0.7652 (mmm160)
REVERT: B  192 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7891 (mm-30)
REVERT: B  195 MET cc_start: 0.7997 (mtp) cc_final: 0.7536 (mtp)
REVERT: B  197 LEU cc_start: 0.9283 (tp) cc_final: 0.8878 (tp)
REVERT: A   74 TYR cc_start: 0.7591 (t80) cc_final: 0.7205 (t80)
REVERT: A  248 GLU cc_start: 0.7390 (mp0) cc_final: 0.7115 (mp0)
REVERT: A  341 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7056 (mm-30)
REVERT: A  344 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8562 (ptmm)
REVERT: A  374 GLN cc_start: 0.8518 (mt0) cc_final: 0.8274 (mm110)
REVERT: A  416 CYS cc_start: 0.8382 (m) cc_final: 0.8056 (m)
REVERT: A  423 ASN cc_start: 0.8386 (p0) cc_final: 0.8086 (p0)
REVERT: A  465 LYS cc_start: 0.7213 (mptt) cc_final: 0.6735 (tptt)
REVERT: A  473 MET cc_start: 0.8564 (mmt) cc_final: 0.8344 (mmt)
REVERT: A  656 ASP cc_start: 0.7549 (m-30) cc_final: 0.7342 (m-30)
  outliers start: 22
  outliers final: 10
  residues processed: 188
  average time/residue: 0.0634
  time to fit residues: 17.0586
Evaluate side-chains
  170 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0470
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.1484

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN
** A 638 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 = 0.3830 r_free = 0.3830 target = 0.155500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.123446 restraints weight = 12736.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.123334 restraints weight = 11988.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124562 restraints weight = 12287.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.125709 restraints weight = 8166.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.126234 restraints weight = 7149.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7437  Z= 0.133
  Angle     :  0.654  10.722  10065  Z= 0.323
  Chirality :  0.040   0.298   1106
  Planarity :  0.004   0.062   1257
  Dihedral  :  4.165  26.150    973
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.94 %
    Favored  : 76.02 %
  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:  1.52 (0.29), residues: 866
  helix:  2.01 (0.20), residues: 657
  sheet:  None (None), residues: 0
  loop : -2.42 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 589 
 TYR   0.016   0.001   TYR A 436 
 PHE   0.030   0.002   PHE B 277 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.003   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7437)
  covalent geometry    : angle       0.65383 (10065)
  hydrogen bonds       : bond        0.04242 (  498)
  hydrogen bonds       : angle       3.78962 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8407 (mt0) cc_final: 0.8068 (tm-30)
REVERT: B   60 THR cc_start: 0.9041 (p) cc_final: 0.8834 (p)
REVERT: B   83 PHE cc_start: 0.6688 (t80) cc_final: 0.6438 (t80)
REVERT: B   85 ARG cc_start: 0.8579 (mmt180) cc_final: 0.7693 (mmm160)
REVERT: B  189 GLN cc_start: 0.8783 (mp10) cc_final: 0.8577 (mp10)
REVERT: B  195 MET cc_start: 0.7768 (mtp) cc_final: 0.7350 (mtp)
REVERT: B  197 LEU cc_start: 0.9284 (tp) cc_final: 0.8916 (tp)
REVERT: B  298 MET cc_start: 0.7957 (mtt) cc_final: 0.7723 (mtt)
REVERT: B  318 TRP cc_start: 0.6470 (t-100) cc_final: 0.5673 (t-100)
REVERT: A  341 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7255 (mm-30)
REVERT: A  344 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8366 (ptmm)
REVERT: A  416 CYS cc_start: 0.8364 (m) cc_final: 0.8091 (m)
REVERT: A  423 ASN cc_start: 0.8292 (p0) cc_final: 0.7198 (t0)
REVERT: A  465 LYS cc_start: 0.7260 (mptt) cc_final: 0.6814 (tptt)
REVERT: A  473 MET cc_start: 0.8511 (mmt) cc_final: 0.8306 (mmt)
REVERT: A  656 ASP cc_start: 0.7614 (m-30) cc_final: 0.7369 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 182
  average time/residue: 0.0686
  time to fit residues: 17.6242
Evaluate side-chains
  174 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 504 ASN
A 620 GLN
A 633 ASN
A 638 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.124697 restraints weight = 12717.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122898 restraints weight = 10811.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.124456 restraints weight = 10660.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.125134 restraints weight = 7329.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.125810 restraints weight = 6822.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7437  Z= 0.139
  Angle     :  0.661  11.380  10065  Z= 0.334
  Chirality :  0.041   0.310   1106
  Planarity :  0.004   0.060   1257
  Dihedral  :  4.143  27.140    973
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.19 %
    Favored  : 75.51 %
  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:  1.57 (0.29), residues: 866
  helix:  2.05 (0.20), residues: 657
  sheet:  None (None), residues: 0
  loop : -2.44 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.015   0.001   TYR A  90 
 PHE   0.039   0.002   PHE B 147 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7437)
  covalent geometry    : angle       0.66126 (10065)
  hydrogen bonds       : bond        0.04336 (  498)
  hydrogen bonds       : angle       3.82811 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8443 (mt0) cc_final: 0.8041 (tm-30)
REVERT: B   83 PHE cc_start: 0.6839 (t80) cc_final: 0.6553 (t80)
REVERT: B   85 ARG cc_start: 0.8622 (mmt180) cc_final: 0.7695 (mmm160)
REVERT: B  189 GLN cc_start: 0.8854 (mp10) cc_final: 0.8606 (mp10)
REVERT: B  192 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: B  195 MET cc_start: 0.7831 (mtp) cc_final: 0.7524 (mtp)
REVERT: B  197 LEU cc_start: 0.9298 (tp) cc_final: 0.8931 (tp)
REVERT: B  318 TRP cc_start: 0.6594 (t-100) cc_final: 0.5765 (t-100)
REVERT: A   74 TYR cc_start: 0.7997 (t80) cc_final: 0.7627 (t80)
REVERT: A  152 MET cc_start: 0.9017 (tpp) cc_final: 0.8637 (tpp)
REVERT: A  248 GLU cc_start: 0.7526 (mp0) cc_final: 0.6933 (mp0)
REVERT: A  341 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7298 (mm-30)
REVERT: A  344 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8585 (ptmm)
REVERT: A  423 ASN cc_start: 0.8362 (p0) cc_final: 0.8154 (p0)
REVERT: A  465 LYS cc_start: 0.7268 (mptt) cc_final: 0.6790 (tptt)
REVERT: A  473 MET cc_start: 0.8542 (mmt) cc_final: 0.8329 (mmt)
REVERT: A  656 ASP cc_start: 0.7586 (m-30) cc_final: 0.7348 (m-30)
  outliers start: 26
  outliers final: 19
  residues processed: 182
  average time/residue: 0.0632
  time to fit residues: 16.2550
Evaluate side-chains
  178 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  638 HIS
Chi-restraints excluded: chain A residue  639 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN
A 638 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.156741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.125671 restraints weight = 12888.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.124225 restraints weight = 10182.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.125448 restraints weight = 10517.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.126389 restraints weight = 7315.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126774 restraints weight = 6536.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7437  Z= 0.133
  Angle     :  0.675  11.904  10065  Z= 0.340
  Chirality :  0.041   0.337   1106
  Planarity :  0.004   0.059   1257
  Dihedral  :  4.150  27.510    973
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.84 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.60 (0.29), residues: 866
  helix:  2.08 (0.20), residues: 657
  sheet:  None (None), residues: 0
  loop : -2.44 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.016   0.001   TYR A  90 
 PHE   0.042   0.002   PHE B 277 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7437)
  covalent geometry    : angle       0.67522 (10065)
  hydrogen bonds       : bond        0.04292 (  498)
  hydrogen bonds       : angle       3.79632 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8464 (mt0) cc_final: 0.8076 (tm-30)
REVERT: B   83 PHE cc_start: 0.6825 (t80) cc_final: 0.6563 (t80)
REVERT: B   85 ARG cc_start: 0.8555 (mmt180) cc_final: 0.7682 (mmm160)
REVERT: B   92 ASN cc_start: 0.8608 (t0) cc_final: 0.8347 (t0)
REVERT: B  189 GLN cc_start: 0.8842 (mp10) cc_final: 0.8591 (mp10)
REVERT: B  192 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: B  195 MET cc_start: 0.7776 (mtp) cc_final: 0.7432 (mtp)
REVERT: B  197 LEU cc_start: 0.9280 (tp) cc_final: 0.8864 (tp)
REVERT: B  318 TRP cc_start: 0.6519 (t-100) cc_final: 0.5686 (t-100)
REVERT: A  152 MET cc_start: 0.8998 (tpp) cc_final: 0.8633 (tpp)
REVERT: A  341 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7269 (mm-30)
REVERT: A  344 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8605 (ptmm)
REVERT: A  465 LYS cc_start: 0.7240 (mptt) cc_final: 0.6778 (tptt)
REVERT: A  656 ASP cc_start: 0.7588 (m-30) cc_final: 0.7337 (m-30)
  outliers start: 21
  outliers final: 18
  residues processed: 176
  average time/residue: 0.0657
  time to fit residues: 16.2785
Evaluate side-chains
  177 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  638 HIS
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
A 638 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.156630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.125111 restraints weight = 12616.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.125313 restraints weight = 10857.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126467 restraints weight = 9394.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.126821 restraints weight = 6446.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.127263 restraints weight = 5902.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7437  Z= 0.139
  Angle     :  0.687  11.129  10065  Z= 0.353
  Chirality :  0.041   0.321   1106
  Planarity :  0.004   0.059   1257
  Dihedral  :  4.144  29.783    973
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.73 %
    Favored  : 73.73 %
  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:  1.62 (0.29), residues: 866
  helix:  2.09 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.42 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  75 
 TYR   0.018   0.001   TYR A  74 
 PHE   0.050   0.001   PHE B 147 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.005   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7437)
  covalent geometry    : angle       0.68689 (10065)
  hydrogen bonds       : bond        0.04331 (  498)
  hydrogen bonds       : angle       3.83053 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.2773 (pmm) cc_final: 0.2164 (ptt)
REVERT: B    9 GLN cc_start: 0.8410 (mt0) cc_final: 0.8032 (tm-30)
REVERT: B   83 PHE cc_start: 0.6634 (t80) cc_final: 0.6431 (t80)
REVERT: B   85 ARG cc_start: 0.8606 (mmt180) cc_final: 0.7727 (mmm160)
REVERT: B   92 ASN cc_start: 0.8521 (t0) cc_final: 0.8222 (t0)
REVERT: B  189 GLN cc_start: 0.8794 (mp10) cc_final: 0.8577 (mp10)
REVERT: B  195 MET cc_start: 0.7727 (mtp) cc_final: 0.7403 (mtp)
REVERT: B  197 LEU cc_start: 0.9261 (tp) cc_final: 0.8848 (tp)
REVERT: B  318 TRP cc_start: 0.6334 (t-100) cc_final: 0.5516 (t-100)
REVERT: A  152 MET cc_start: 0.9019 (tpp) cc_final: 0.8637 (tpp)
REVERT: A  340 CYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7320 (t)
REVERT: A  341 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7136 (mm-30)
REVERT: A  344 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8649 (ptmm)
REVERT: A  465 LYS cc_start: 0.7218 (mptt) cc_final: 0.6765 (tptt)
REVERT: A  656 ASP cc_start: 0.7543 (m-30) cc_final: 0.7308 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 169
  average time/residue: 0.0651
  time to fit residues: 15.4811
Evaluate side-chains
  173 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  638 HIS
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.3980
   chunk 29 optimal weight:    6.9990
   chunk 36 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0270
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.6642

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
A 638 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127299 restraints weight = 12749.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126792 restraints weight = 10326.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.127697 restraints weight = 9846.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.128329 restraints weight = 6598.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.128760 restraints weight = 5897.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7437  Z= 0.138
  Angle     :  0.718  12.397  10065  Z= 0.364
  Chirality :  0.041   0.318   1106
  Planarity :  0.004   0.059   1257
  Dihedral  :  4.182  29.965    973
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 24.62 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.65 (0.29), residues: 866
  helix:  2.10 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.40 (0.40), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.020   0.001   TYR A  74 
 PHE   0.043   0.002   PHE B 277 
 TRP   0.007   0.001   TRP B 305 
 HIS   0.005   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7437)
  covalent geometry    : angle       0.71779 (10065)
  hydrogen bonds       : bond        0.04280 (  498)
  hydrogen bonds       : angle       3.85835 ( 1488)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.2703 (pmm) cc_final: 0.2104 (ptt)
REVERT: B    9 GLN cc_start: 0.8429 (mt0) cc_final: 0.8023 (tm-30)
REVERT: B   58 ASN cc_start: 0.7689 (t0) cc_final: 0.7306 (t0)
REVERT: B   83 PHE cc_start: 0.6766 (t80) cc_final: 0.6553 (t80)
REVERT: B   85 ARG cc_start: 0.8750 (mmt180) cc_final: 0.7815 (mmm160)
REVERT: B  197 LEU cc_start: 0.9291 (tp) cc_final: 0.8895 (tp)
REVERT: B  318 TRP cc_start: 0.6428 (t-100) cc_final: 0.5602 (t-100)
REVERT: A  132 GLU cc_start: 0.7641 (tp30) cc_final: 0.7038 (tt0)
REVERT: A  340 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7279 (t)
REVERT: A  341 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6976 (mm-30)
REVERT: A  344 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8648 (ptmm)
REVERT: A  465 LYS cc_start: 0.7161 (mptt) cc_final: 0.6709 (tptt)
REVERT: A  534 ASP cc_start: 0.7979 (t70) cc_final: 0.7663 (t0)
REVERT: A  656 ASP cc_start: 0.7513 (m-30) cc_final: 0.7279 (m-30)
  outliers start: 18
  outliers final: 16
  residues processed: 173
  average time/residue: 0.0667
  time to fit residues: 16.3593
Evaluate side-chains
  176 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  638 HIS
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 153 ASN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.150364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.118510 restraints weight = 12780.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.119113 restraints weight = 12000.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119956 restraints weight = 11191.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120543 restraints weight = 7703.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.120980 restraints weight = 7131.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7437  Z= 0.249
  Angle     :  0.816  12.391  10065  Z= 0.419
  Chirality :  0.046   0.311   1106
  Planarity :  0.005   0.053   1257
  Dihedral  :  4.588  29.560    973
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.75 %
    Favored  : 72.46 %
  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:  1.07 (0.28), residues: 866
  helix:  1.69 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.60 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 167 
 TYR   0.021   0.002   TYR A  74 
 PHE   0.053   0.003   PHE B 147 
 TRP   0.012   0.002   TRP A 684 
 HIS   0.007   0.001   HIS A 638 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 7437)
  covalent geometry    : angle       0.81556 (10065)
  hydrogen bonds       : bond        0.05282 (  498)
  hydrogen bonds       : angle       4.37531 ( 1488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1114.14 seconds
wall clock time: 19 minutes 58.71 seconds (1198.71 seconds total)