Starting phenix.real_space_refine
on Fri Aug 22 13:38:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gjn_40095/08_2025/8gjn_40095.cif"
  }
  resolution = 3.6
  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=   0.011
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      15      5.16       5
     C    2102      2.51       5
     N     550      2.21       5
     O     652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3319
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 934
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "B"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.89, per 1000 atoms: 0.27
  Number of scatterers: 3319
  At special positions: 0
  Unit cell: (86.625, 54.45, 107.25, 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      15     16.00
     O     652      8.00
     N     550      7.00
     C    2102      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  43 " - pdb=" SG  CYS B 108 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 130.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 8 sheets defined
      13.1% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 3.719A  pdb=" N   TYR A  51 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
      removed outlier: 4.450A  pdb=" N   GLY A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.758A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 4.106A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 389
      removed outlier: 4.074A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 411
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
      removed outlier: 3.661A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 6.213A  pdb=" N   GLU A  29 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   MET A  53 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY A  69 " --> pdb=" O   MET A  53 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   TRP A  55 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26
      removed outlier: 4.157A  pdb=" N   VAL B  39 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33
      removed outlier: 6.388A  pdb=" N   TRP B  55 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392
    Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454

    108 hydrogen bonds defined for protein.
    249 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: 0.35

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 801
        1.33 -     1.46: 791
        1.46 -     1.58: 1791
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3401
  Sorted by residual:
  bond pdb=" N   ILE C 472 "
       pdb=" CA  ILE C 472 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.19e-02 7.06e+03 1.14e+01
  bond pdb=" N   CYS A 115 "
       pdb=" CA  CYS A 115 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.17e-02 7.31e+03 1.12e+01
  bond pdb=" N   VAL A  37 "
       pdb=" CA  VAL A  37 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.17e-02 7.31e+03 1.04e+01
  bond pdb=" N   ARG C 457 "
       pdb=" CA  ARG C 457 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.037 1.18e-02 7.18e+03 9.94e+00
  bond pdb=" N   VAL C 524 "
       pdb=" CA  VAL C 524 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.10e-02 8.26e+03 9.93e+00
  ... (remaining 3396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 3361
        1.75 -     3.50: 1059
        3.50 -     5.25: 180
        5.25 -     7.00: 13
        7.00 -     8.75: 2
  Bond angle restraints: 4615
  Sorted by residual:
  angle pdb=" N   PHE C 490 "
        pdb=" CA  PHE C 490 "
        pdb=" C   PHE C 490 "
      ideal   model   delta    sigma   weight residual
     109.24  100.49    8.75 1.39e+00 5.18e-01 3.96e+01
  angle pdb=" N   CYS C 488 "
        pdb=" CA  CYS C 488 "
        pdb=" C   CYS C 488 "
      ideal   model   delta    sigma   weight residual
     109.54  101.74    7.80 1.37e+00 5.33e-01 3.25e+01
  angle pdb=" N   TYR C 489 "
        pdb=" CA  TYR C 489 "
        pdb=" C   TYR C 489 "
      ideal   model   delta    sigma   weight residual
     110.43  116.65   -6.22 1.31e+00 5.83e-01 2.25e+01
  angle pdb=" C   GLY A  27 "
        pdb=" N   PRO A  28 "
        pdb=" CA  PRO A  28 "
      ideal   model   delta    sigma   weight residual
     119.90  124.65   -4.75 1.02e+00 9.61e-01 2.16e+01
  angle pdb=" C   LYS B  80 "
        pdb=" CA  LYS B  80 "
        pdb=" CB  LYS B  80 "
      ideal   model   delta    sigma   weight residual
     116.54  111.44    5.10 1.15e+00 7.56e-01 1.97e+01
  ... (remaining 4610 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 1851
       17.49 -    34.98: 134
       34.98 -    52.47: 21
       52.47 -    69.95: 21
       69.95 -    87.44: 2
  Dihedral angle restraints: 2029
    sinusoidal: 809
      harmonic: 1220
  Sorted by residual:
  dihedral pdb=" CA  ASP B  61 "
           pdb=" C   ASP B  61 "
           pdb=" N   GLY B  62 "
           pdb=" CA  GLY B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.37   29.63     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CA  SER B  97 "
           pdb=" C   SER B  97 "
           pdb=" N   PRO B  98 "
           pdb=" CA  PRO B  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.41   26.59     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  ALA A 111 "
           pdb=" C   ALA A 111 "
           pdb=" N   VAL A 112 "
           pdb=" CA  VAL A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.44   26.56     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 2026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 226
       0.060 -    0.120: 168
       0.120 -    0.180: 80
       0.180 -    0.240: 17
       0.240 -    0.300: 5
  Chirality restraints: 496
  Sorted by residual:
  chirality pdb=" CA  PHE C 464 "
            pdb=" N   PHE C 464 "
            pdb=" C   PHE C 464 "
            pdb=" CB  PHE C 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  PRO A  33 "
            pdb=" N   PRO A  33 "
            pdb=" C   PRO A  33 "
            pdb=" CB  PRO A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  LEU C 461 "
            pdb=" N   LEU C 461 "
            pdb=" C   LEU C 461 "
            pdb=" CB  LEU C 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 493 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 601 "   -0.104 2.00e-02 2.50e+03   8.66e-02 9.37e+01
        pdb=" C7  NAG C 601 "    0.024 2.00e-02 2.50e+03
        pdb=" C8  NAG C 601 "   -0.076 2.00e-02 2.50e+03
        pdb=" N2  NAG C 601 "    0.142 2.00e-02 2.50e+03
        pdb=" O7  NAG C 601 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 380 "   -0.094 2.00e-02 2.50e+03   5.01e-02 5.01e+01
        pdb=" CG  TYR C 380 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 380 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 380 "    0.037 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 380 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 380 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 380 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR C 380 "   -0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  69 "   -0.071 2.00e-02 2.50e+03   4.07e-02 3.31e+01
        pdb=" CG  TYR B  69 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  69 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  69 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  69 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  69 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  69 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B  69 "   -0.063 2.00e-02 2.50e+03
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 1409
        2.92 -     3.42: 3062
        3.42 -     3.91: 5638
        3.91 -     4.41: 6166
        4.41 -     4.90: 10475
  Nonbonded interactions: 26750
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 111 "
            pdb=" OG1 THR C 478 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" OG1 THR C 333 "
            pdb=" N   ASN C 334 "
     model   vdw
     2.451 3.120
  nonbonded pdb=" O   GLN A  24 "
            pdb=" N   LYS A  42 "
     model   vdw
     2.470 3.120
  nonbonded pdb=" OH  TYR C 453 "
            pdb=" OE1 GLN C 493 "
     model   vdw
     2.482 3.040
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.506 3.040
  ... (remaining 26745 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:             6.310
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.400
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
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      :  0.013   0.046   3408  Z= 0.826
  Angle     :  1.677  18.886   4630  Z= 1.123
  Chirality :  0.093   0.300    496
  Planarity :  0.013   0.098    595
  Dihedral  : 14.166  87.440   1237
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.40 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.37), residues: 415
  helix: -3.89 (0.58), residues: 26
  sheet: -1.56 (0.46), residues: 116
  loop : -1.77 (0.33), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 509 
 TYR   0.094   0.014   TYR C 380 
 PHE   0.062   0.008   PHE C 464 
 TRP   0.046   0.009   TRP C 353 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.01277 ( 3401)
  covalent geometry    : angle       1.64806 ( 4615)
  SS BOND              : bond        0.00970 (    6)
  SS BOND              : angle       1.34600 (   12)
  hydrogen bonds       : bond        0.20146 (  103)
  hydrogen bonds       : angle      10.18995 (  249)
  link_NAG-ASN         : bond        0.00815 (    1)
  link_NAG-ASN         : angle      12.49374 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.7469 (tttt) cc_final: 0.7225 (tttt)
REVERT: C  367 VAL cc_start: 0.8406 (t) cc_final: 0.8095 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0619
  time to fit residues: 5.3555
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0770
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.2536

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A  62 GLN
B  57 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.164437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137597 restraints weight = 5857.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.141710 restraints weight = 3042.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.144342 restraints weight = 1867.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.146072 restraints weight = 1278.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147201 restraints weight = 960.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3408  Z= 0.133
  Angle     :  0.597   8.790   4630  Z= 0.311
  Chirality :  0.043   0.194    496
  Planarity :  0.004   0.032    595
  Dihedral  :  5.312  35.063    488
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.68 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.39), residues: 415
  helix: -3.77 (0.63), residues: 27
  sheet: -1.24 (0.45), residues: 133
  loop : -0.85 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 117 
 TYR   0.017   0.001   TYR C 380 
 PHE   0.015   0.002   PHE C 497 
 TRP   0.013   0.002   TRP C 353 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3401)
  covalent geometry    : angle       0.59255 ( 4615)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       0.95474 (   12)
  hydrogen bonds       : bond        0.03870 (  103)
  hydrogen bonds       : angle       7.69475 (  249)
  link_NAG-ASN         : bond        0.00301 (    1)
  link_NAG-ASN         : angle       2.36364 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 SER cc_start: 0.6762 (p) cc_final: 0.6551 (p)
REVERT: C  492 LEU cc_start: 0.8398 (mp) cc_final: 0.8179 (mp)
REVERT: C  508 TYR cc_start: 0.8648 (m-10) cc_final: 0.8392 (m-10)
  outliers start: 7
  outliers final: 5
  residues processed: 74
  average time/residue: 0.0494
  time to fit residues: 4.7361
Evaluate side-chains
  75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0000
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
B  57 GLN
C 360 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.162155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.135295 restraints weight = 5872.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.139478 restraints weight = 3096.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.142117 restraints weight = 1934.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143868 restraints weight = 1348.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.144847 restraints weight = 1022.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
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      :  0.004   0.026   3408  Z= 0.166
  Angle     :  0.574   7.179   4630  Z= 0.300
  Chirality :  0.043   0.198    496
  Planarity :  0.004   0.041    595
  Dihedral  :  5.060  38.692    488
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.52 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.39), residues: 415
  helix: -3.12 (0.79), residues: 28
  sheet: -0.96 (0.44), residues: 139
  loop : -0.77 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 457 
 TYR   0.020   0.002   TYR C 423 
 PHE   0.011   0.002   PHE C 497 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3401)
  covalent geometry    : angle       0.57195 ( 4615)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       0.75626 (   12)
  hydrogen bonds       : bond        0.03559 (  103)
  hydrogen bonds       : angle       7.40791 (  249)
  link_NAG-ASN         : bond        0.00117 (    1)
  link_NAG-ASN         : angle       1.68042 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 SER cc_start: 0.7824 (p) cc_final: 0.7534 (p)
REVERT: C  367 VAL cc_start: 0.8380 (t) cc_final: 0.8154 (p)
REVERT: C  438 SER cc_start: 0.8696 (m) cc_final: 0.8078 (p)
REVERT: C  503 VAL cc_start: 0.8295 (t) cc_final: 0.7911 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0414
  time to fit residues: 4.5507
Evaluate side-chains
  88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.0270
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A  71 ASN
C 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.160737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.134179 restraints weight = 5719.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138318 restraints weight = 3000.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.140946 restraints weight = 1870.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.142624 restraints weight = 1301.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.143652 restraints weight = 989.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3408  Z= 0.177
  Angle     :  0.578   9.508   4630  Z= 0.293
  Chirality :  0.043   0.222    496
  Planarity :  0.004   0.040    595
  Dihedral  :  5.109  34.828    488
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.26 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.39), residues: 415
  helix: -2.95 (0.75), residues: 34
  sheet: -0.87 (0.43), residues: 144
  loop : -0.93 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 117 
 TYR   0.019   0.002   TYR C 423 
 PHE   0.009   0.002   PHE C 486 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3401)
  covalent geometry    : angle       0.57685 ( 4615)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       0.69365 (   12)
  hydrogen bonds       : bond        0.03338 (  103)
  hydrogen bonds       : angle       7.25451 (  249)
  link_NAG-ASN         : bond        0.00109 (    1)
  link_NAG-ASN         : angle       1.57906 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8104 (p-80)
REVERT: C  370 ASN cc_start: 0.8075 (m-40) cc_final: 0.7784 (m-40)
REVERT: C  478 THR cc_start: 0.8179 (m) cc_final: 0.7856 (p)
REVERT: C  503 VAL cc_start: 0.8348 (t) cc_final: 0.7969 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.0421
  time to fit residues: 4.3513
Evaluate side-chains
  73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 SER
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0000
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0040
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
B 110 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.159282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.132757 restraints weight = 5748.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.136885 restraints weight = 3030.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139501 restraints weight = 1890.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.141172 restraints weight = 1317.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.142232 restraints weight = 1002.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3408  Z= 0.199
  Angle     :  0.587   7.350   4630  Z= 0.298
  Chirality :  0.043   0.232    496
  Planarity :  0.004   0.040    595
  Dihedral  :  5.290  37.662    488
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.08 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.70 (0.39), residues: 415
  helix: -2.98 (0.76), residues: 34
  sheet: -0.93 (0.42), residues: 147
  loop : -0.88 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 357 
 TYR   0.017   0.002   TYR C 423 
 PHE   0.009   0.001   PHE C 400 
 TRP   0.008   0.001   TRP A  55 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3401)
  covalent geometry    : angle       0.58451 ( 4615)
  SS BOND              : bond        0.00381 (    6)
  SS BOND              : angle       0.89269 (   12)
  hydrogen bonds       : bond        0.03353 (  103)
  hydrogen bonds       : angle       7.35238 (  249)
  link_NAG-ASN         : bond        0.00180 (    1)
  link_NAG-ASN         : angle       1.60345 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8146 (p-80)
REVERT: B   65 LYS cc_start: 0.7470 (tttt) cc_final: 0.7255 (tttt)
REVERT: C  478 THR cc_start: 0.8140 (m) cc_final: 0.7840 (p)
REVERT: C  487 ASN cc_start: 0.7986 (m-40) cc_final: 0.7762 (m110)
  outliers start: 13
  outliers final: 12
  residues processed: 81
  average time/residue: 0.0358
  time to fit residues: 3.8518
Evaluate side-chains
  74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 SER
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  511 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0020
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.2980
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
** C 422 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.160479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.134482 restraints weight = 5765.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.138687 restraints weight = 2981.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.141337 restraints weight = 1837.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.143001 restraints weight = 1269.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.143815 restraints weight = 960.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3408  Z= 0.134
  Angle     :  0.552   7.655   4630  Z= 0.276
  Chirality :  0.042   0.230    496
  Planarity :  0.004   0.039    595
  Dihedral  :  4.896  33.796    488
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.08 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.40), residues: 415
  helix: -3.04 (0.72), residues: 34
  sheet: -0.76 (0.43), residues: 142
  loop : -0.77 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 357 
 TYR   0.019   0.001   TYR C 423 
 PHE   0.008   0.001   PHE C 400 
 TRP   0.008   0.001   TRP C 436 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3401)
  covalent geometry    : angle       0.55091 ( 4615)
  SS BOND              : bond        0.00261 (    6)
  SS BOND              : angle       0.75562 (   12)
  hydrogen bonds       : bond        0.03000 (  103)
  hydrogen bonds       : angle       7.07443 (  249)
  link_NAG-ASN         : bond        0.00024 (    1)
  link_NAG-ASN         : angle       1.29881 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.7425 (tttt) cc_final: 0.7200 (tttt)
REVERT: C  478 THR cc_start: 0.8118 (m) cc_final: 0.7798 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0520
  time to fit residues: 4.8398
Evaluate side-chains
  73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
** C 422 ASN ** 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 = 0.4106 r_free = 0.4106 target = 0.161206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135051 restraints weight = 5882.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.139295 restraints weight = 3063.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.142006 restraints weight = 1894.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143704 restraints weight = 1313.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.144692 restraints weight = 995.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3408  Z= 0.134
  Angle     :  0.546   8.142   4630  Z= 0.274
  Chirality :  0.042   0.240    496
  Planarity :  0.004   0.039    595
  Dihedral  :  4.830  33.735    488
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 16.99 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.40), residues: 415
  helix: -3.11 (0.70), residues: 34
  sheet: -0.77 (0.43), residues: 144
  loop : -0.74 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 357 
 TYR   0.009   0.001   TYR B 106 
 PHE   0.008   0.001   PHE C 400 
 TRP   0.011   0.001   TRP A 128 
 HIS   0.000   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3401)
  covalent geometry    : angle       0.54501 ( 4615)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       0.67837 (   12)
  hydrogen bonds       : bond        0.03070 (  103)
  hydrogen bonds       : angle       7.09566 (  249)
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.36951 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.8179 (p-80)
REVERT: B   65 LYS cc_start: 0.7405 (tttt) cc_final: 0.7190 (tttt)
REVERT: C  478 THR cc_start: 0.8099 (m) cc_final: 0.7775 (p)
  outliers start: 14
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0521
  time to fit residues: 4.8123
Evaluate side-chains
  71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  511 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 39 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0470
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.2078

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
** C 422 ASN ** 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 = 0.4124 r_free = 0.4124 target = 0.162589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.136787 restraints weight = 5960.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.141048 restraints weight = 3089.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.143733 restraints weight = 1906.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.145409 restraints weight = 1312.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.146517 restraints weight = 991.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3408  Z= 0.110
  Angle     :  0.539   8.641   4630  Z= 0.269
  Chirality :  0.042   0.235    496
  Planarity :  0.004   0.035    595
  Dihedral  :  4.596  31.326    488
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.36 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.40), residues: 415
  helix: -3.14 (0.68), residues: 34
  sheet: -0.58 (0.43), residues: 139
  loop : -0.67 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 357 
 TYR   0.008   0.001   TYR C 423 
 PHE   0.008   0.001   PHE B  82 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3401)
  covalent geometry    : angle       0.53797 ( 4615)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       0.55119 (   12)
  hydrogen bonds       : bond        0.02979 (  103)
  hydrogen bonds       : angle       6.99440 (  249)
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       1.20802 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  478 THR cc_start: 0.8020 (m) cc_final: 0.7656 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0508
  time to fit residues: 4.3507
Evaluate side-chains
  68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  511 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0670
   chunk 36 optimal weight:    0.2980
   chunk 21 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.160790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.134910 restraints weight = 5801.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.139217 restraints weight = 3021.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.141871 restraints weight = 1862.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.143557 restraints weight = 1283.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.144586 restraints weight = 964.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3408  Z= 0.156
  Angle     :  0.581   8.795   4630  Z= 0.286
  Chirality :  0.043   0.252    496
  Planarity :  0.004   0.035    595
  Dihedral  :  4.861  35.103    488
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.36 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.40), residues: 415
  helix: -3.11 (0.70), residues: 34
  sheet: -0.70 (0.42), residues: 145
  loop : -0.71 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 357 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.009   0.001   PHE C 400 
 TRP   0.014   0.002   TRP A 128 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3401)
  covalent geometry    : angle       0.57951 ( 4615)
  SS BOND              : bond        0.00219 (    6)
  SS BOND              : angle       0.58454 (   12)
  hydrogen bonds       : bond        0.03154 (  103)
  hydrogen bonds       : angle       7.14358 (  249)
  link_NAG-ASN         : bond        0.00082 (    1)
  link_NAG-ASN         : angle       1.64019 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.7404 (tttt) cc_final: 0.7162 (tttt)
REVERT: C  478 THR cc_start: 0.8095 (m) cc_final: 0.7766 (p)
  outliers start: 10
  outliers final: 8
  residues processed: 67
  average time/residue: 0.0493
  time to fit residues: 4.2671
Evaluate side-chains
  70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 35 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0670
   chunk 9 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.1314

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

Flipped N/Q/H residues before XYZ refinement:
** B  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.163941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.138536 restraints weight = 5854.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.142798 restraints weight = 3032.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.145441 restraints weight = 1862.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147127 restraints weight = 1280.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.148203 restraints weight = 963.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3408  Z= 0.099
  Angle     :  0.553   8.800   4630  Z= 0.273
  Chirality :  0.041   0.130    496
  Planarity :  0.004   0.034    595
  Dihedral  :  4.511  29.743    488
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.63 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.40), residues: 415
  helix: -3.08 (0.66), residues: 34
  sheet: -0.42 (0.43), residues: 137
  loop : -0.62 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  44 
 TYR   0.006   0.001   TYR C 423 
 PHE   0.007   0.001   PHE C 497 
 TRP   0.011   0.001   TRP A 128 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3401)
  covalent geometry    : angle       0.55252 ( 4615)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       0.52482 (   12)
  hydrogen bonds       : bond        0.02901 (  103)
  hydrogen bonds       : angle       6.91819 (  249)
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       1.06806 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6362 (m)
REVERT: C  370 ASN cc_start: 0.8097 (m-40) cc_final: 0.7782 (m-40)
REVERT: C  423 TYR cc_start: 0.8558 (t80) cc_final: 0.7998 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0552
  time to fit residues: 4.7473
Evaluate side-chains
  70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 37 optimal weight:    0.0050
   chunk 26 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0030
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.164873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139026 restraints weight = 6013.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.143301 restraints weight = 3139.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146001 restraints weight = 1948.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.147775 restraints weight = 1345.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.148780 restraints weight = 1013.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.4881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3408  Z= 0.096
  Angle     :  0.542   8.737   4630  Z= 0.266
  Chirality :  0.043   0.285    496
  Planarity :  0.004   0.034    595
  Dihedral  :  4.310  27.534    488
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.36 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.41), residues: 415
  helix: -2.77 (0.80), residues: 27
  sheet: -0.35 (0.43), residues: 137
  loop : -0.59 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.010   0.001   TYR C 380 
 PHE   0.008   0.001   PHE C 377 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.000   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 3401)
  covalent geometry    : angle       0.54153 ( 4615)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.50831 (   12)
  hydrogen bonds       : bond        0.02765 (  103)
  hydrogen bonds       : angle       6.81223 (  249)
  link_NAG-ASN         : bond        0.00149 (    1)
  link_NAG-ASN         : angle       1.11610 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 893.60 seconds
wall clock time: 16 minutes 3.21 seconds (963.21 seconds total)