Starting phenix.real_space_refine
on Tue Mar  3 13:03:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2026/7eya_31380.map"
  }
  resolution = 3.77
  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=   0.022
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      18      5.16       5
     C    2970      2.51       5
     N     756      2.21       5
     O     885      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 4629
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "L"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 801
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 965
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
    Chain: "N"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1359
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 8, 'TRANS': 156}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.07, per 1000 atoms: 0.23
  Number of scatterers: 4629
  At special positions: 0
  Unit cell: (73.03, 95.92, 98.1, 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      18     16.00
     O     885      8.00
     N     756      7.00
     C    2970      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 131 " - pdb=" SG  CYS N 166 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN N 165 "
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 291.0 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:  1066

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 11 sheets defined
      9.4% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 337 through 343
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.533A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 390
      removed outlier: 4.456A  pdb=" N   ASN R 388 " --> pdb=" O   THR R 385 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU R 390 " --> pdb=" O   LEU R 387 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 410
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'R' and resid 438 through 443
    Processing helix  chain 'R' and resid 502 through 506
    Processing helix  chain 'H' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358
      removed outlier: 4.287A  pdb=" N   ASN R 394 " --> pdb=" O   GLU R 516 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU R 516 " --> pdb=" O   ASN R 394 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY R 431 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   TYR R 380 " --> pdb=" O   GLY R 431 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL R 433 " --> pdb=" O   LYS R 378 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LYS R 378 " --> pdb=" O   VAL R 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6
      removed outlier: 3.535A  pdb=" N   PHE L  71 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 46
      removed outlier: 3.577A  pdb=" N   GLN L  89 " --> pdb=" O   ALA L  34 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.598A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.598A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 45 through 51
      removed outlier: 6.750A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 29 through 31
    Processing sheet with id=AA9, first strand: chain 'N' and resid 50 through 51
      removed outlier: 4.109A  pdb=" N   ASP N 287 " --> pdb=" O   LYS N 278 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 84 through 85
      removed outlier: 3.547A  pdb=" N   SER N 172 " --> pdb=" O   VAL N 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 224 through 229
      removed outlier: 5.988A  pdb=" N   SER N 205 " --> pdb=" O   PRO N 225 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL N 227 " --> pdb=" O   ILE N 203 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    303 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: 0.65

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 730
        1.25 -     1.40: 1345
        1.40 -     1.55: 2650
        1.55 -     1.70: 1
        1.70 -     1.84: 23
  Bond restraints: 4749
  Sorted by residual:
  bond pdb=" CG  PRO R 507 "
       pdb=" CD  PRO R 507 "
    ideal  model  delta    sigma   weight residual
    1.503  1.107  0.396 3.40e-02 8.65e+02 1.36e+02
  bond pdb=" CB  PRO R 507 "
       pdb=" CG  PRO R 507 "
    ideal  model  delta    sigma   weight residual
    1.492  1.155  0.337 5.00e-02 4.00e+02 4.54e+01
  bond pdb=" N   PRO R 507 "
       pdb=" CD  PRO R 507 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 5.80e+00
  bond pdb=" C1  BMA A   3 "
       pdb=" C2  BMA A   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.553 -0.034 2.00e-02 2.50e+03 2.82e+00
  bond pdb=" N   PRO R 507 "
       pdb=" CA  PRO R 507 "
    ideal  model  delta    sigma   weight residual
    1.467  1.486 -0.019 1.21e-02 6.83e+03 2.55e+00
  ... (remaining 4744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.20: 6441
        9.20 -    18.40: 0
       18.40 -    27.60: 2
       27.60 -    36.80: 0
       36.80 -    46.00: 1
  Bond angle restraints: 6444
  Sorted by residual:
  angle pdb=" N   PRO R 507 "
        pdb=" CD  PRO R 507 "
        pdb=" CG  PRO R 507 "
      ideal   model   delta    sigma   weight residual
     103.20   76.09   27.11 1.50e+00 4.44e-01 3.27e+02
  angle pdb=" CB  PRO R 507 "
        pdb=" CG  PRO R 507 "
        pdb=" CD  PRO R 507 "
      ideal   model   delta    sigma   weight residual
     106.10  152.10  -46.00 3.20e+00 9.77e-02 2.07e+02
  angle pdb=" CA  PRO R 507 "
        pdb=" CB  PRO R 507 "
        pdb=" CG  PRO R 507 "
      ideal   model   delta    sigma   weight residual
     104.50   79.51   24.99 1.90e+00 2.77e-01 1.73e+02
  angle pdb=" CA  PRO R 507 "
        pdb=" N   PRO R 507 "
        pdb=" CD  PRO R 507 "
      ideal   model   delta    sigma   weight residual
     112.00  102.91    9.09 1.40e+00 5.10e-01 4.22e+01
  angle pdb=" C   ASN N 165 "
        pdb=" CA  ASN N 165 "
        pdb=" CB  ASN N 165 "
      ideal   model   delta    sigma   weight residual
     117.23  110.39    6.84 1.36e+00 5.41e-01 2.53e+01
  ... (remaining 6439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.17: 2587
       22.17 -    44.34: 160
       44.34 -    66.50: 21
       66.50 -    88.67: 13
       88.67 -   110.84: 12
  Dihedral angle restraints: 2793
    sinusoidal: 1120
      harmonic: 1673
  Sorted by residual:
  dihedral pdb=" CA  PHE L  94 "
           pdb=" C   PHE L  94 "
           pdb=" N   PRO L  95 "
           pdb=" CA  PRO L  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.96   45.04     0      5.00e+00 4.00e-02 8.12e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.63  -71.63     1      1.00e+01 1.00e-02 6.57e+01
  dihedral pdb=" CA  SER L   7 "
           pdb=" C   SER L   7 "
           pdb=" N   PRO L   8 "
           pdb=" CA  PRO L   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.26   39.74     0      5.00e+00 4.00e-02 6.32e+01
  ... (remaining 2790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 584
       0.054 -    0.109: 90
       0.109 -    0.163: 21
       0.163 -    0.217: 1
       0.217 -    0.272: 1
  Chirality restraints: 697
  Sorted by residual:
  chirality pdb=" C5  BMA A   3 "
            pdb=" C4  BMA A   3 "
            pdb=" C6  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  CYS N 166 "
            pdb=" N   CYS N 166 "
            pdb=" C   CYS N 166 "
            pdb=" CB  CYS N 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality pdb=" CB  VAL H  64 "
            pdb=" CA  VAL H  64 "
            pdb=" CG1 VAL H  64 "
            pdb=" CG2 VAL H  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 694 not shown)

  Planarity restraints: 820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN R 506 "    0.057 5.00e-02 4.00e+02   7.98e-02 1.02e+01
        pdb=" N   PRO R 507 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO R 507 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO R 507 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR N  38 "    0.047 5.00e-02 4.00e+02   7.17e-02 8.23e+00
        pdb=" N   PRO N  39 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO N  39 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO N  39 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L  94 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO L  95 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 817 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 122
        2.69 -     3.24: 4233
        3.24 -     3.80: 6527
        3.80 -     4.35: 8655
        4.35 -     4.90: 14738
  Nonbonded interactions: 34275
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  40 "
            pdb=" OH  TYR N 204 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" O   ASN R 439 "
            pdb=" OG  SER R 443 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   GLN H   3 "
            pdb=" OG  SER H  25 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OD1 ASN R 439 "
            pdb=" OG  SER R 443 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR N  91 "
            pdb=" OE1 GLU N 191 "
     model   vdw
     2.232 3.040
  ... (remaining 34270 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:             2.390
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.160
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
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      :  0.008   0.396   4758  Z= 0.238
  Angle     :  1.013  46.004   6465  Z= 0.498
  Chirality :  0.043   0.272    697
  Planarity :  0.006   0.080    819
  Dihedral  : 16.975 110.839   1709
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.58 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.30 (0.35), residues: 554
  helix: -2.80 (0.87), residues: 25
  sheet: -0.56 (0.40), residues: 186
  loop : -2.09 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 355 
 TYR   0.023   0.001   TYR H 102 
 PHE   0.013   0.001   PHE R 456 
 TRP   0.008   0.001   TRP L  35 
 HIS   0.001   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00798 ( 4749)
  covalent geometry    : angle       1.00534 ( 6444)
  SS BOND              : bond        0.00673 (    6)
  SS BOND              : angle       1.40206 (   12)
  hydrogen bonds       : bond        0.27208 (  123)
  hydrogen bonds       : angle      10.14844 (  303)
  link_BETA1-4         : bond        0.01091 (    2)
  link_BETA1-4         : angle       2.47138 (    6)
  link_NAG-ASN         : bond        0.00072 (    1)
  link_NAG-ASN         : angle       4.33599 (    3)

*********************** 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
  115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.180 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8217 (p) cc_final: 0.7686 (p)
REVERT: H   83 MET cc_start: 0.6305 (ptt) cc_final: 0.6073 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0608
  time to fit residues: 9.3742
Evaluate side-chains
  94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 498 GLN
H   3 GLN
H  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.156643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136025 restraints weight = 6589.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138717 restraints weight = 9344.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.138770 restraints weight = 4826.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138591 restraints weight = 5051.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.139275 restraints weight = 3915.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   4758  Z= 0.240
  Angle     :  0.740   9.550   6465  Z= 0.390
  Chirality :  0.048   0.206    697
  Planarity :  0.007   0.072    819
  Dihedral  : 13.931  92.205    694
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.03 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.76 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.25 (0.35), residues: 554
  helix: -2.72 (1.05), residues: 19
  sheet: -0.54 (0.40), residues: 185
  loop : -2.07 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 100 
 TYR   0.020   0.002   TYR H  95 
 PHE   0.029   0.002   PHE N  43 
 TRP   0.012   0.002   TRP R 353 
 HIS   0.003   0.001   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 4749)
  covalent geometry    : angle       0.72739 ( 6444)
  SS BOND              : bond        0.00739 (    6)
  SS BOND              : angle       1.95332 (   12)
  hydrogen bonds       : bond        0.05395 (  123)
  hydrogen bonds       : angle       7.30444 (  303)
  link_BETA1-4         : bond        0.00244 (    2)
  link_BETA1-4         : angle       3.05370 (    6)
  link_NAG-ASN         : bond        0.00514 (    1)
  link_NAG-ASN         : angle       3.30963 (    3)

*********************** 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
  108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.180 
Fit side-chains
REVERT: R  418 ILE cc_start: 0.9061 (tt) cc_final: 0.8753 (tt)
REVERT: R  438 SER cc_start: 0.8118 (p) cc_final: 0.7589 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0608
  time to fit residues: 8.1923
Evaluate side-chains
  100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  197 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 498 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.159393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137499 restraints weight = 6573.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.141259 restraints weight = 9024.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141078 restraints weight = 4400.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.141036 restraints weight = 4166.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142197 restraints weight = 3555.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4758  Z= 0.122
  Angle     :  0.652   9.253   6465  Z= 0.333
  Chirality :  0.045   0.257    697
  Planarity :  0.006   0.066    819
  Dihedral  : 11.316  80.869    694
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.22 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.94 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.08 (0.36), residues: 554
  helix: -2.65 (1.16), residues: 19
  sheet: -0.31 (0.40), residues: 188
  loop : -2.04 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 100 
 TYR   0.013   0.001   TYR R 380 
 PHE   0.033   0.002   PHE R 456 
 TRP   0.007   0.001   TRP R 436 
 HIS   0.001   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4749)
  covalent geometry    : angle       0.63849 ( 6444)
  SS BOND              : bond        0.00649 (    6)
  SS BOND              : angle       1.59195 (   12)
  hydrogen bonds       : bond        0.03886 (  123)
  hydrogen bonds       : angle       6.45670 (  303)
  link_BETA1-4         : bond        0.00352 (    2)
  link_BETA1-4         : angle       3.49844 (    6)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       2.25608 (    3)

*********************** 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
  103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.149 
Fit side-chains
REVERT: R  355 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7490 (ttt180)
REVERT: R  418 ILE cc_start: 0.9115 (tt) cc_final: 0.8840 (tt)
REVERT: R  438 SER cc_start: 0.8079 (p) cc_final: 0.7598 (p)
  outliers start: 6
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0669
  time to fit residues: 8.7180
Evaluate side-chains
  96 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  130 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
R 498 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.158455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.134330 restraints weight = 6544.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.137179 restraints weight = 9340.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138786 restraints weight = 5622.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.138445 restraints weight = 4578.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.139686 restraints weight = 4030.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4758  Z= 0.176
  Angle     :  0.685  10.534   6465  Z= 0.348
  Chirality :  0.046   0.262    697
  Planarity :  0.006   0.072    819
  Dihedral  : 10.118  73.524    694
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.48 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.14 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.12 (0.36), residues: 554
  helix: -2.60 (1.13), residues: 19
  sheet: -0.40 (0.39), residues: 193
  loop : -2.05 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  19 
 TYR   0.018   0.001   TYR H  95 
 PHE   0.034   0.002   PHE R 456 
 TRP   0.010   0.001   TRP R 353 
 HIS   0.003   0.001   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 4749)
  covalent geometry    : angle       0.67127 ( 6444)
  SS BOND              : bond        0.00595 (    6)
  SS BOND              : angle       1.61237 (   12)
  hydrogen bonds       : bond        0.04018 (  123)
  hydrogen bonds       : angle       6.14356 (  303)
  link_BETA1-4         : bond        0.00297 (    2)
  link_BETA1-4         : angle       3.60461 (    6)
  link_NAG-ASN         : bond        0.00021 (    1)
  link_NAG-ASN         : angle       2.48380 (    3)

*********************** 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
  109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.170 
Fit side-chains
REVERT: R  418 ILE cc_start: 0.9175 (tt) cc_final: 0.8953 (tt)
REVERT: R  438 SER cc_start: 0.8160 (p) cc_final: 0.7572 (p)
REVERT: R  498 GLN cc_start: 0.7653 (mt0) cc_final: 0.7366 (mt0)
REVERT: R  508 TYR cc_start: 0.8340 (m-10) cc_final: 0.7891 (m-10)
REVERT: N   58 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7645 (m-80)
REVERT: N  169 GLU cc_start: 0.7550 (mp0) cc_final: 0.7079 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0638
  time to fit residues: 8.6826
Evaluate side-chains
  102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 44 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0570
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.159688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.135492 restraints weight = 6482.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138702 restraints weight = 9130.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.139760 restraints weight = 5321.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.140001 restraints weight = 4020.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140737 restraints weight = 3855.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4758  Z= 0.130
  Angle     :  0.663   8.683   6465  Z= 0.332
  Chirality :  0.045   0.272    697
  Planarity :  0.005   0.065    819
  Dihedral  :  9.413  68.097    694
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.68 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.33 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.03 (0.36), residues: 554
  helix: -2.39 (1.15), residues: 19
  sheet: -0.39 (0.39), residues: 200
  loop : -1.99 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.035   0.002   PHE R 456 
 TRP   0.008   0.001   TRP L   3 
 HIS   0.002   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4749)
  covalent geometry    : angle       0.65050 ( 6444)
  SS BOND              : bond        0.00557 (    6)
  SS BOND              : angle       1.45082 (   12)
  hydrogen bonds       : bond        0.03527 (  123)
  hydrogen bonds       : angle       5.94146 (  303)
  link_BETA1-4         : bond        0.00289 (    2)
  link_BETA1-4         : angle       3.46537 (    6)
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       2.52418 (    3)

*********************** 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
  109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.166 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8102 (p) cc_final: 0.7522 (p)
REVERT: R  498 GLN cc_start: 0.7677 (mt0) cc_final: 0.7437 (mt0)
REVERT: R  508 TYR cc_start: 0.8308 (m-10) cc_final: 0.7890 (m-10)
REVERT: H  121 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.5685 (pm20)
REVERT: N   58 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7408 (m-80)
REVERT: N  169 GLU cc_start: 0.7506 (mp0) cc_final: 0.7047 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0640
  time to fit residues: 8.7445
Evaluate side-chains
  103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  121 GLN
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0010
   chunk 46 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0670
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4324

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.177432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.151851 restraints weight = 6579.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.153458 restraints weight = 7659.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156135 restraints weight = 6292.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156196 restraints weight = 4278.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.156651 restraints weight = 4773.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4758  Z= 0.119
  Angle     :  0.648   8.804   6465  Z= 0.324
  Chirality :  0.044   0.258    697
  Planarity :  0.005   0.069    819
  Dihedral  :  8.650  61.606    694
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.22 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.14 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.36), residues: 554
  helix: -2.19 (1.15), residues: 19
  sheet: -0.27 (0.39), residues: 204
  loop : -1.92 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  19 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.029   0.002   PHE R 456 
 TRP   0.007   0.001   TRP L   3 
 HIS   0.001   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4749)
  covalent geometry    : angle       0.63421 ( 6444)
  SS BOND              : bond        0.00600 (    6)
  SS BOND              : angle       1.59670 (   12)
  hydrogen bonds       : bond        0.03308 (  123)
  hydrogen bonds       : angle       5.70416 (  303)
  link_BETA1-4         : bond        0.00332 (    2)
  link_BETA1-4         : angle       3.45915 (    6)
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       2.64137 (    3)

*********************** 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
  107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.231 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8161 (p) cc_final: 0.7600 (p)
REVERT: R  498 GLN cc_start: 0.7577 (mt0) cc_final: 0.7314 (mt0)
REVERT: R  508 TYR cc_start: 0.8289 (m-10) cc_final: 0.8061 (m-80)
REVERT: H  121 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.5750 (pm20)
REVERT: N   58 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7391 (m-80)
REVERT: N  169 GLU cc_start: 0.7521 (mp0) cc_final: 0.6968 (mp0)
  outliers start: 15
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0613
  time to fit residues: 8.0150
Evaluate side-chains
  103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  121 GLN
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0060
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
L  27 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.177165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151559 restraints weight = 6556.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.152646 restraints weight = 7361.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.154945 restraints weight = 6238.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.155328 restraints weight = 4297.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155851 restraints weight = 4791.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4758  Z= 0.129
  Angle     :  0.670  12.099   6465  Z= 0.330
  Chirality :  0.044   0.248    697
  Planarity :  0.005   0.066    819
  Dihedral  :  8.033  54.748    694
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.58 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.14 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.36), residues: 554
  helix: -2.18 (1.15), residues: 19
  sheet: -0.27 (0.38), residues: 206
  loop : -1.97 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.013   0.001   TYR H  95 
 PHE   0.023   0.002   PHE R 456 
 TRP   0.007   0.001   TRP R 353 
 HIS   0.002   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4749)
  covalent geometry    : angle       0.65576 ( 6444)
  SS BOND              : bond        0.00605 (    6)
  SS BOND              : angle       1.50900 (   12)
  hydrogen bonds       : bond        0.03285 (  123)
  hydrogen bonds       : angle       5.61282 (  303)
  link_BETA1-4         : bond        0.00320 (    2)
  link_BETA1-4         : angle       3.68340 (    6)
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       2.81629 (    3)

*********************** 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
  106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.186 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8172 (p) cc_final: 0.7714 (p)
REVERT: R  508 TYR cc_start: 0.8327 (m-10) cc_final: 0.8078 (m-80)
REVERT: H  121 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5847 (pm20)
REVERT: N   58 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7439 (m-80)
REVERT: N  169 GLU cc_start: 0.7550 (mp0) cc_final: 0.6949 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 100
  average time/residue: 0.0630
  time to fit residues: 8.2715
Evaluate side-chains
  102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  121 GLN
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
R 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.160381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.135645 restraints weight = 6580.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138456 restraints weight = 8778.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.140379 restraints weight = 6065.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.140412 restraints weight = 4855.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141513 restraints weight = 4710.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4758  Z= 0.134
  Angle     :  0.680  12.936   6465  Z= 0.334
  Chirality :  0.044   0.222    697
  Planarity :  0.005   0.069    819
  Dihedral  :  7.357  46.242    694
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.94 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.33 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.37), residues: 554
  helix: -2.14 (1.15), residues: 19
  sheet: -0.21 (0.39), residues: 204
  loop : -1.92 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  19 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.023   0.001   PHE N  43 
 TRP   0.008   0.001   TRP R 353 
 HIS   0.002   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4749)
  covalent geometry    : angle       0.66538 ( 6444)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       1.42755 (   12)
  hydrogen bonds       : bond        0.03332 (  123)
  hydrogen bonds       : angle       5.56409 (  303)
  link_BETA1-4         : bond        0.00261 (    2)
  link_BETA1-4         : angle       3.88154 (    6)
  link_NAG-ASN         : bond        0.00126 (    1)
  link_NAG-ASN         : angle       2.91376 (    3)

*********************** 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
  109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.152 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8207 (p) cc_final: 0.7669 (p)
REVERT: R  508 TYR cc_start: 0.8343 (m-10) cc_final: 0.8078 (m-80)
REVERT: H  121 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.5825 (pm20)
REVERT: N   58 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7457 (m-80)
REVERT: N  169 GLU cc_start: 0.7544 (mp0) cc_final: 0.6965 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0561
  time to fit residues: 7.7476
Evaluate side-chains
  103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  121 GLN
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    0.0010
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 29 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0980
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.162544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.140218 restraints weight = 6447.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.142185 restraints weight = 9919.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.143957 restraints weight = 6203.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.143359 restraints weight = 5604.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.144113 restraints weight = 4548.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4758  Z= 0.107
  Angle     :  0.675  13.100   6465  Z= 0.328
  Chirality :  0.044   0.194    697
  Planarity :  0.005   0.065    819
  Dihedral  :  6.415  44.957    694
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.58 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.73 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.37), residues: 554
  helix: -2.10 (1.16), residues: 19
  sheet: -0.18 (0.39), residues: 205
  loop : -1.85 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  19 
 TYR   0.017   0.001   TYR R 501 
 PHE   0.021   0.001   PHE N  43 
 TRP   0.006   0.001   TRP R 436 
 HIS   0.001   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4749)
  covalent geometry    : angle       0.65950 ( 6444)
  SS BOND              : bond        0.00546 (    6)
  SS BOND              : angle       1.28690 (   12)
  hydrogen bonds       : bond        0.02992 (  123)
  hydrogen bonds       : angle       5.42417 (  303)
  link_BETA1-4         : bond        0.00260 (    2)
  link_BETA1-4         : angle       3.99733 (    6)
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       2.94371 (    3)

*********************** 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
  105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.137 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8190 (p) cc_final: 0.7683 (p)
REVERT: R  508 TYR cc_start: 0.8211 (m-10) cc_final: 0.7961 (m-80)
REVERT: L   36 TYR cc_start: 0.8830 (m-80) cc_final: 0.8579 (m-80)
REVERT: N  169 GLU cc_start: 0.7426 (mp0) cc_final: 0.6877 (mp0)
  outliers start: 13
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0544
  time to fit residues: 7.2181
Evaluate side-chains
  101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0870
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
R 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.160115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137002 restraints weight = 6593.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.139924 restraints weight = 9358.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.140818 restraints weight = 5043.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140552 restraints weight = 4645.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141270 restraints weight = 3919.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4758  Z= 0.142
  Angle     :  0.691  12.878   6465  Z= 0.342
  Chirality :  0.044   0.185    697
  Planarity :  0.006   0.080    819
  Dihedral  :  5.426  46.004    694
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.12 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.73 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.37), residues: 554
  helix: -2.38 (0.91), residues: 27
  sheet: -0.12 (0.39), residues: 200
  loop : -1.94 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  19 
 TYR   0.018   0.001   TYR R 501 
 PHE   0.024   0.002   PHE N  43 
 TRP   0.008   0.001   TRP N  64 
 HIS   0.002   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4749)
  covalent geometry    : angle       0.67393 ( 6444)
  SS BOND              : bond        0.00599 (    6)
  SS BOND              : angle       1.40490 (   12)
  hydrogen bonds       : bond        0.03439 (  123)
  hydrogen bonds       : angle       5.43431 (  303)
  link_BETA1-4         : bond        0.00444 (    2)
  link_BETA1-4         : angle       4.20123 (    6)
  link_NAG-ASN         : bond        0.00084 (    1)
  link_NAG-ASN         : angle       3.09048 (    3)

********************** 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
  105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.171 
Fit side-chains
REVERT: R  438 SER cc_start: 0.8116 (p) cc_final: 0.7711 (p)
REVERT: R  508 TYR cc_start: 0.8285 (m-10) cc_final: 0.7969 (m-80)
REVERT: H   82 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.6895 (tp-100)
REVERT: N   58 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7415 (m-80)
REVERT: N  169 GLU cc_start: 0.7546 (mp0) cc_final: 0.6947 (mp0)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0526
  time to fit residues: 7.1261
Evaluate side-chains
  102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  498 GLN
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   82 GLN
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain N residue   58 PHE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  274 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0570
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0970
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
R 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.160655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136096 restraints weight = 6617.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.139385 restraints weight = 8792.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140669 restraints weight = 5439.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.140975 restraints weight = 4041.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141770 restraints weight = 3876.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4758  Z= 0.121
  Angle     :  0.677  12.771   6465  Z= 0.335
  Chirality :  0.044   0.186    697
  Planarity :  0.006   0.074    819
  Dihedral  :  5.201  45.682    694
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.40 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.33 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.37), residues: 554
  helix: -2.38 (0.90), residues: 27
  sheet: -0.20 (0.38), residues: 205
  loop : -1.87 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  19 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.023   0.001   PHE N  43 
 TRP   0.006   0.001   TRP R 353 
 HIS   0.001   0.000   HIS H  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4749)
  covalent geometry    : angle       0.65973 ( 6444)
  SS BOND              : bond        0.00579 (    6)
  SS BOND              : angle       1.32879 (   12)
  hydrogen bonds       : bond        0.03184 (  123)
  hydrogen bonds       : angle       5.40409 (  303)
  link_BETA1-4         : bond        0.00457 (    2)
  link_BETA1-4         : angle       4.04860 (    6)
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       3.41137 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 995.28 seconds
wall clock time: 17 minutes 46.05 seconds (1066.05 seconds total)