Starting phenix.real_space_refine
on Tue Mar  3 12:44:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r0o_53486/03_2026/9r0o_53486.map"
  }
  resolution = 3.1
  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=   0.009
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      36      5.16       5
     C    2830      2.51       5
     N     706      2.21       5
     O     756      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 4328
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4308
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 558, 4299
          Classifications: {'peptide': 558}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 524}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 558, 4299
          Classifications: {'peptide': 558}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 524}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4402
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'TCW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.64, per 1000 atoms: 0.38
  Number of scatterers: 4328
  At special positions: 0
  Unit cell: (84.912, 96.624, 73.932, 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      36     16.00
     O     756      8.00
     N     706      7.00
     C    2830      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 492 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 594 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 697.6 milliseconds
  

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      72.6% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 30 through 64
      removed outlier: 3.675A  pdb=" N   PHE A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   THR A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 91
      removed outlier: 3.974A  pdb=" N   ASN A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ILE A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 96 through 122
      removed outlier: 3.668A  pdb=" N   THR A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      Proline residue:  A 118  - end of helix
    Processing helix  chain 'A' and resid 164 through 185
    Processing helix  chain 'A' and resid 186 through 199
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.986A  pdb=" N   PHE A 217 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 230
    Processing helix  chain 'A' and resid 256 through 273
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 307 through 313
    Processing helix  chain 'A' and resid 313 through 323
    Processing helix  chain 'A' and resid 324 through 357
      removed outlier: 5.111A  pdb=" N   ASN A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   LYS A 350 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 370
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 394 through 412
      removed outlier: 4.239A  pdb=" N   ARG A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 416
    Processing helix  chain 'A' and resid 442 through 446
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 514 through 530
    Processing helix  chain 'A' and resid 532 through 544
      removed outlier: 3.839A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 564
      removed outlier: 4.405A  pdb=" N   PHE A 551 " --> pdb=" O   ASP A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 579
      removed outlier: 4.166A  pdb=" N   SER A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 635
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466
      removed outlier: 4.022A  pdb=" N   ILE A 488 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER A 476 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585
      removed outlier: 5.143A  pdb=" N   CYS A 580 " --> pdb=" O   TYR A 596 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   TYR A 596 " --> pdb=" O   CYS A 580 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ARG A 582 " --> pdb=" O   CYS A 594 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   CYS A 594 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ASN A 584 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 1286
        1.34 -     1.47: 1190
        1.47 -     1.60: 1915
        1.60 -     1.74: 0
        1.74 -     1.87: 52
  Bond restraints: 4443
  Sorted by residual:
  bond pdb=" CB  CYS A 492 "
       pdb=" SG  CYS A 492 "
    ideal  model  delta    sigma   weight residual
    1.808  1.869 -0.061 3.30e-02 9.18e+02 3.44e+00
  bond pdb=" N   CYS A  23 "
       pdb=" CA  CYS A  23 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.15e+00
  bond pdb=" N   VAL A 390 "
       pdb=" CA  VAL A 390 "
    ideal  model  delta    sigma   weight residual
    1.474  1.461  0.014 1.57e-02 4.06e+03 7.46e-01
  bond pdb=" CG  LEU A 178 "
       pdb=" CD1 LEU A 178 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.16e-01
  bond pdb=" C   SER A 122 "
       pdb=" N   GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.323  1.335 -0.013 1.64e-02 3.72e+03 5.89e-01
  ... (remaining 4438 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.93: 5631
        0.93 -     1.85: 323
        1.85 -     2.78: 50
        2.78 -     3.70: 25
        3.70 -     4.63: 13
  Bond angle restraints: 6042
  Sorted by residual:
  angle pdb=" N   ILE A 436 "
        pdb=" CA  ILE A 436 "
        pdb=" C   ILE A 436 "
      ideal   model   delta    sigma   weight residual
     111.45  108.79    2.66 9.30e-01 1.16e+00 8.21e+00
  angle pdb=" C   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" CB  VAL A 185 "
      ideal   model   delta    sigma   weight residual
     114.00  110.53    3.47 1.31e+00 5.83e-01 7.02e+00
  angle pdb=" NE BARG A 561 "
        pdb=" CZ BARG A 561 "
        pdb=" NH2BARG A 561 "
      ideal   model   delta    sigma   weight residual
     119.20  121.47   -2.27 9.00e-01 1.23e+00 6.37e+00
  angle pdb=" C   THR A 184 "
        pdb=" N   VAL A 185 "
        pdb=" CA  VAL A 185 "
      ideal   model   delta    sigma   weight residual
     120.33  122.08   -1.75 8.00e-01 1.56e+00 4.76e+00
  angle pdb=" NE BARG A 561 "
        pdb=" CZ BARG A 561 "
        pdb=" NH1BARG A 561 "
      ideal   model   delta    sigma   weight residual
     121.50  119.33    2.17 1.00e+00 1.00e+00 4.69e+00
  ... (remaining 6037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2363
       17.69 -    35.39: 202
       35.39 -    53.08: 55
       53.08 -    70.77: 9
       70.77 -    88.47: 3
  Dihedral angle restraints: 2632
    sinusoidal: 1013
      harmonic: 1619
  Sorted by residual:
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 507 "
           pdb=" CB  CYS A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.81  -66.81     1      1.00e+01 1.00e-02 5.82e+01
  dihedral pdb=" CB  CYS A 419 "
           pdb=" SG  CYS A 419 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.42   41.58     1      1.00e+01 1.00e-02 2.42e+01
  dihedral pdb=" CB  CYS A 450 "
           pdb=" SG  CYS A 450 "
           pdb=" SG  CYS A 470 "
           pdb=" CB  CYS A 470 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.07  -37.93     1      1.00e+01 1.00e-02 2.03e+01
  ... (remaining 2629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 425
       0.028 -    0.055: 170
       0.055 -    0.083: 58
       0.083 -    0.111: 32
       0.111 -    0.138: 5
  Chirality restraints: 690
  Sorted by residual:
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  VAL A 424 "
            pdb=" N   VAL A 424 "
            pdb=" C   VAL A 424 "
            pdb=" CB  VAL A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  VAL A 458 "
            pdb=" N   VAL A 458 "
            pdb=" C   VAL A 458 "
            pdb=" CB  VAL A 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 687 not shown)

  Planarity restraints: 754
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 412 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO A 413 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 123 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO A 124 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 124 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 124 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 117 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO A 118 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 751 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 23
        2.60 -     3.17: 3845
        3.17 -     3.75: 6764
        3.75 -     4.32: 8891
        4.32 -     4.90: 15481
  Nonbonded interactions: 35004
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  85 "
            pdb=" OG  SER A  89 "
     model   vdw
     2.021 3.040
  nonbonded pdb=" OE1 GLN A 334 "
            pdb=" NE2 GLN A 556 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" OH  TYR A  51 "
            pdb=" O   TRP A 257 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR A 356 "
            pdb=" OG  SER A 518 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" N   SER A 247 "
            pdb=" OD2 ASP A 250 "
     model   vdw
     2.406 3.120
  ... (remaining 34999 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.41 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.700
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.060
  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:   13.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
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   0.061   4449  Z= 0.141
  Angle     :  0.554   6.186   6054  Z= 0.302
  Chirality :  0.038   0.138    690
  Planarity :  0.005   0.034    754
  Dihedral  : 14.415  88.468   1574
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 11.95 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.52 (0.37), residues: 554
  helix:  2.26 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop :  0.65 (0.47), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  97 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.011   0.001   PHE A 318 
 TRP   0.008   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4443)
  covalent geometry    : angle       0.54336 ( 6042)
  SS BOND              : bond        0.00632 (    6)
  SS BOND              : angle       2.46933 (   12)
  hydrogen bonds       : bond        0.15222 (  298)
  hydrogen bonds       : angle       5.97694 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6029 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 98
  average time/residue: 0.0688
  time to fit residues: 8.6950
Evaluate side-chains
  60 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 GLN
A 349 ASN
A 355 GLN
A 534 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.132982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.105174 restraints weight = 13582.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 3.69
r_work: 0.3452 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4449  Z= 0.161
  Angle     :  0.659  10.127   6054  Z= 0.334
  Chirality :  0.043   0.162    690
  Planarity :  0.005   0.043    754
  Dihedral  :  4.258  31.645    610
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.93 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.57 (0.36), residues: 554
  helix:  2.28 (0.27), residues: 365
  sheet:  None (None), residues: 0
  loop :  0.67 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 252 
 TYR   0.014   0.001   TYR A 606 
 PHE   0.032   0.001   PHE A 347 
 TRP   0.012   0.001   TRP A 253 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4443)
  covalent geometry    : angle       0.64388 ( 6042)
  SS BOND              : bond        0.00415 (    6)
  SS BOND              : angle       3.20013 (   12)
  hydrogen bonds       : bond        0.04591 (  298)
  hydrogen bonds       : angle       4.63848 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 GLU cc_start: 0.8578 (mp0) cc_final: 0.8361 (mp0)
REVERT: A  165 GLU cc_start: 0.6675 (mt-10) cc_final: 0.5706 (tm-30)
REVERT: A  166 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8731 (p)
REVERT: A  188 GLN cc_start: 0.8466 (mp10) cc_final: 0.8047 (mp10)
  outliers start: 12
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0608
  time to fit residues: 6.1527
Evaluate side-chains
  63 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 52 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.133658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.105807 restraints weight = 13986.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 3.84
r_work: 0.3460 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4449  Z= 0.139
  Angle     :  0.586   7.463   6054  Z= 0.293
  Chirality :  0.041   0.160    690
  Planarity :  0.005   0.041    754
  Dihedral  :  3.929  29.777    607
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.56 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.82 (0.37), residues: 554
  helix:  2.44 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop :  0.82 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 252 
 TYR   0.013   0.001   TYR A 634 
 PHE   0.036   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 253 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4443)
  covalent geometry    : angle       0.57921 ( 6042)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       2.05481 (   12)
  hydrogen bonds       : bond        0.04073 (  298)
  hydrogen bonds       : angle       4.33385 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 GLU cc_start: 0.8590 (mp0) cc_final: 0.8349 (mp0)
REVERT: A  116 THR cc_start: 0.8422 (m) cc_final: 0.8051 (p)
REVERT: A  165 GLU cc_start: 0.6716 (mt-10) cc_final: 0.5687 (tm-30)
REVERT: A  166 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8732 (p)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0474
  time to fit residues: 4.9450
Evaluate side-chains
  67 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.137499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.107765 restraints weight = 14618.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.95
r_work: 0.3561 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4449  Z= 0.157
  Angle     :  0.587   6.548   6054  Z= 0.290
  Chirality :  0.042   0.143    690
  Planarity :  0.005   0.040    754
  Dihedral  :  3.959  31.001    607
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.98 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.90 (0.37), residues: 554
  helix:  2.50 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop :  0.87 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 590 
 TYR   0.010   0.001   TYR A 606 
 PHE   0.012   0.001   PHE A 391 
 TRP   0.008   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4443)
  covalent geometry    : angle       0.58141 ( 6042)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       1.87759 (   12)
  hydrogen bonds       : bond        0.03983 (  298)
  hydrogen bonds       : angle       4.24704 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8446 (mp0) cc_final: 0.8170 (mp0)
REVERT: A  165 GLU cc_start: 0.6850 (mt-10) cc_final: 0.5793 (tm-30)
REVERT: A  166 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8758 (p)
REVERT: A  454 PHE cc_start: 0.5952 (m-80) cc_final: 0.5154 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0559
  time to fit residues: 5.6531
Evaluate side-chains
  70 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 51 optimal weight:    0.1980
   chunk 40 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0670
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.134024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.106099 restraints weight = 14018.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 3.87
r_work: 0.3419 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4449  Z= 0.134
  Angle     :  0.570   6.723   6054  Z= 0.280
  Chirality :  0.041   0.171    690
  Planarity :  0.005   0.042    754
  Dihedral  :  3.890  29.004    607
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.98 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.12 (0.37), residues: 554
  helix:  2.74 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop :  0.87 (0.49), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 590 
 TYR   0.009   0.001   TYR A 606 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4443)
  covalent geometry    : angle       0.56528 ( 6042)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       1.70943 (   12)
  hydrogen bonds       : bond        0.03728 (  298)
  hydrogen bonds       : angle       4.13168 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8641 (mp0) cc_final: 0.8273 (mp0)
REVERT: A  116 THR cc_start: 0.8386 (m) cc_final: 0.7976 (p)
REVERT: A  165 GLU cc_start: 0.6847 (mt-10) cc_final: 0.5768 (tm-30)
REVERT: A  454 PHE cc_start: 0.5858 (m-80) cc_final: 0.5031 (m-80)
REVERT: A  547 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0529
  time to fit residues: 5.7293
Evaluate side-chains
  71 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 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 = 0.3954 r_free = 0.3954 target = 0.133442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.105176 restraints weight = 15945.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 4.13
r_work: 0.3406 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4449  Z= 0.140
  Angle     :  0.580   9.443   6054  Z= 0.281
  Chirality :  0.042   0.158    690
  Planarity :  0.005   0.040    754
  Dihedral  :  3.911  29.094    607
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.14 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.09 (0.37), residues: 554
  helix:  2.69 (0.27), residues: 361
  sheet:  None (None), residues: 0
  loop :  0.90 (0.49), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.009   0.001   TYR A 194 
 PHE   0.011   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4443)
  covalent geometry    : angle       0.57551 ( 6042)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       1.70264 (   12)
  hydrogen bonds       : bond        0.03693 (  298)
  hydrogen bonds       : angle       4.15892 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8624 (mp0) cc_final: 0.8260 (mp0)
REVERT: A  116 THR cc_start: 0.8377 (m) cc_final: 0.7971 (p)
REVERT: A  165 GLU cc_start: 0.6632 (mt-10) cc_final: 0.5595 (tm-30)
REVERT: A  267 PHE cc_start: 0.8667 (m-80) cc_final: 0.8431 (m-80)
REVERT: A  426 GLU cc_start: 0.7801 (tp30) cc_final: 0.7523 (tp30)
REVERT: A  454 PHE cc_start: 0.5773 (m-80) cc_final: 0.4969 (m-80)
REVERT: A  465 GLU cc_start: 0.7724 (tt0) cc_final: 0.7509 (mt-10)
  outliers start: 14
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0492
  time to fit residues: 5.0064
Evaluate side-chains
  70 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.133984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.107361 restraints weight = 8474.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.05
r_work: 0.3472 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4449  Z= 0.128
  Angle     :  0.568   7.998   6054  Z= 0.274
  Chirality :  0.041   0.134    690
  Planarity :  0.005   0.041    754
  Dihedral  :  3.872  28.278    607
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.77 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.15 (0.37), residues: 554
  helix:  2.71 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop :  0.92 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.009   0.001   TYR A 606 
 PHE   0.011   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4443)
  covalent geometry    : angle       0.56398 ( 6042)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       1.60066 (   12)
  hydrogen bonds       : bond        0.03617 (  298)
  hydrogen bonds       : angle       4.11448 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8579 (mp0) cc_final: 0.8230 (mp0)
REVERT: A  116 THR cc_start: 0.8303 (m) cc_final: 0.7901 (p)
REVERT: A  165 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5539 (tm-30)
REVERT: A  426 GLU cc_start: 0.7781 (tp30) cc_final: 0.7463 (tp30)
REVERT: A  454 PHE cc_start: 0.5750 (m-80) cc_final: 0.4943 (m-80)
REVERT: A  542 ARG cc_start: 0.8061 (mpt180) cc_final: 0.7775 (mpt180)
  outliers start: 11
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0519
  time to fit residues: 5.3532
Evaluate side-chains
  68 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0170
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.134315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104865 restraints weight = 19669.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 4.67
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4449  Z= 0.125
  Angle     :  0.579   7.760   6054  Z= 0.279
  Chirality :  0.042   0.228    690
  Planarity :  0.005   0.041    754
  Dihedral  :  3.854  27.476    607
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.56 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.20 (0.37), residues: 554
  helix:  2.76 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop :  0.92 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.008   0.001   TYR A 597 
 PHE   0.016   0.001   PHE A 557 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4443)
  covalent geometry    : angle       0.57539 ( 6042)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       1.52372 (   12)
  hydrogen bonds       : bond        0.03585 (  298)
  hydrogen bonds       : angle       4.07633 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7722 (pp20) cc_final: 0.7486 (pp20)
REVERT: A   78 GLU cc_start: 0.8629 (mp0) cc_final: 0.8254 (mp0)
REVERT: A  116 THR cc_start: 0.8188 (m) cc_final: 0.7804 (p)
REVERT: A  165 GLU cc_start: 0.6733 (mt-10) cc_final: 0.5567 (tm-30)
REVERT: A  426 GLU cc_start: 0.7781 (tp30) cc_final: 0.7446 (tp30)
REVERT: A  454 PHE cc_start: 0.5660 (m-80) cc_final: 0.4838 (m-80)
REVERT: A  542 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7422 (mpt180)
REVERT: A  611 MET cc_start: 0.8916 (mmt) cc_final: 0.8559 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0498
  time to fit residues: 5.1920
Evaluate side-chains
  72 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 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 = 0.3937 r_free = 0.3937 target = 0.132265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.102622 restraints weight = 19743.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 4.69
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4449  Z= 0.161
  Angle     :  0.605   8.307   6054  Z= 0.292
  Chirality :  0.042   0.133    690
  Planarity :  0.005   0.040    754
  Dihedral  :  3.962  30.304    607
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.77 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.16 (0.37), residues: 554
  helix:  2.78 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop :  0.86 (0.49), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.014   0.001   TYR A 194 
 PHE   0.015   0.001   PHE A 557 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4443)
  covalent geometry    : angle       0.60048 ( 6042)
  SS BOND              : bond        0.00192 (    6)
  SS BOND              : angle       1.69525 (   12)
  hydrogen bonds       : bond        0.03900 (  298)
  hydrogen bonds       : angle       4.18870 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7811 (pp20) cc_final: 0.7579 (pp20)
REVERT: A   78 GLU cc_start: 0.8640 (mp0) cc_final: 0.8261 (mp0)
REVERT: A  165 GLU cc_start: 0.6748 (mt-10) cc_final: 0.5590 (tm-30)
REVERT: A  426 GLU cc_start: 0.7789 (tp30) cc_final: 0.7453 (tp30)
REVERT: A  454 PHE cc_start: 0.5605 (m-80) cc_final: 0.4761 (m-80)
REVERT: A  542 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7388 (mpt180)
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0465
  time to fit residues: 4.7048
Evaluate side-chains
  69 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 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 = 0.3943 r_free = 0.3943 target = 0.132680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104563 restraints weight = 14048.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 3.94
r_work: 0.3401 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4449  Z= 0.148
  Angle     :  0.596   7.576   6054  Z= 0.288
  Chirality :  0.042   0.132    690
  Planarity :  0.005   0.041    754
  Dihedral  :  3.947  30.288    607
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.40 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.07 (0.37), residues: 554
  helix:  2.68 (0.27), residues: 365
  sheet:  None (None), residues: 0
  loop :  0.83 (0.49), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.009   0.001   TYR A 194 
 PHE   0.015   0.001   PHE A 557 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4443)
  covalent geometry    : angle       0.59329 ( 6042)
  SS BOND              : bond        0.00174 (    6)
  SS BOND              : angle       1.44423 (   12)
  hydrogen bonds       : bond        0.03823 (  298)
  hydrogen bonds       : angle       4.14247 (  870)

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

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

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1108 Ramachandran restraints generated.
    554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7918 (pp20) cc_final: 0.7696 (pp20)
REVERT: A   78 GLU cc_start: 0.8625 (mp0) cc_final: 0.8265 (mp0)
REVERT: A  165 GLU cc_start: 0.6525 (mt-10) cc_final: 0.5537 (tm-30)
REVERT: A  426 GLU cc_start: 0.7891 (tp30) cc_final: 0.7566 (tp30)
REVERT: A  454 PHE cc_start: 0.5637 (m-80) cc_final: 0.4819 (m-80)
REVERT: A  542 ARG cc_start: 0.8226 (mpt180) cc_final: 0.7943 (mpt180)
  outliers start: 11
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0501
  time to fit residues: 4.8982
Evaluate side-chains
  70 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  631 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0870
   chunk 9 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.133478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.104497 restraints weight = 19482.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 4.67
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4449  Z= 0.132
  Angle     :  0.575   7.557   6054  Z= 0.277
  Chirality :  0.041   0.133    690
  Planarity :  0.005   0.041    754
  Dihedral  :  3.888  29.172    607
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.40 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  3.17 (0.37), residues: 554
  helix:  2.74 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop :  0.89 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 590 
 TYR   0.009   0.001   TYR A 606 
 PHE   0.016   0.001   PHE A 557 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4443)
  covalent geometry    : angle       0.57420 ( 6042)
  SS BOND              : bond        0.00149 (    6)
  SS BOND              : angle       1.02260 (   12)
  hydrogen bonds       : bond        0.03722 (  298)
  hydrogen bonds       : angle       4.08509 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1334.38 seconds
wall clock time: 23 minutes 27.31 seconds (1407.31 seconds total)