Starting phenix.real_space_refine
on Thu Jul 24 00:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_31380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_31380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_31380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_31380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2025/7eya_31380.cif"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.13, per 1000 atoms: 0.89
  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: 1.22
  Conformation dependent library (CDL) restraints added in 526.9 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: 0.60
  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: 1.22

  Time building geometry restraints manager: 1.32 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:             5.930
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.090
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.210
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.008   0.001   TRP L  35 
 HIS   0.001   0.000   HIS H  59 
 PHE   0.013   0.001   PHE R 456 
 TYR   0.023   0.001   TYR H 102 
 ARG   0.004   0.000   ARG R 355 

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

*********************** 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  : 0.508 
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: 0.1392
  time to fit residues: 21.0396
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  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0170
   chunk 22 optimal weight:    0.0770
   chunk 43 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.3576

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.160378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.137525 restraints weight = 6544.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.140077 restraints weight = 9571.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141461 restraints weight = 6626.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4758  Z= 0.126
  Angle     :  0.684   9.172   6465  Z= 0.351
  Chirality :  0.045   0.249    697
  Planarity :  0.006   0.068    819
  Dihedral  : 12.329  84.867    694
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.04 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.36 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.35), residues: 554
  helix: -2.99 (0.88), residues: 25
  sheet: -0.32 (0.41), residues: 181
  loop : -2.00 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L  35 
 HIS   0.001   0.000   HIS H  59 
 PHE   0.026   0.002   PHE N  43 
 TYR   0.016   0.001   TYR R 380 
 ARG   0.009   0.001   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    1)
  link_NAG-ASN         : angle       2.66377 (    3)
  link_BETA1-4         : bond        0.00122 (    2)
  link_BETA1-4         : angle       3.40038 (    6)
  hydrogen bonds       : bond        0.03841 (  123)
  hydrogen bonds       : angle       6.93906 (  303)
  SS BOND              : bond        0.00686 (    6)
  SS BOND              : angle       1.66156 (   12)
  covalent geometry    : bond        0.00289 ( 4749)
  covalent geometry    : angle       0.67044 ( 6444)

*********************** 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
  112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.491 
Fit side-chains
REVERT: R  418 ILE cc_start: 0.9036 (tt) cc_final: 0.8755 (tt)
REVERT: R  438 SER cc_start: 0.8049 (p) cc_final: 0.7524 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 109
  average time/residue: 0.1421
  time to fit residues: 20.2516
Evaluate side-chains
  100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain N residue  130 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0050
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.160403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137561 restraints weight = 6497.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139570 restraints weight = 8895.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140607 restraints weight = 6763.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1787

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= 0.120
  Angle     :  0.646   8.962   6465  Z= 0.327
  Chirality :  0.045   0.266    697
  Planarity :  0.005   0.066    819
  Dihedral  : 10.415  76.103    694
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.14 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.15 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.36), residues: 554
  helix: -2.70 (1.18), residues: 19
  sheet: -0.21 (0.40), residues: 187
  loop : -1.97 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.028   0.002   PHE R 456 
 TYR   0.016   0.001   TYR R 380 
 ARG   0.005   0.001   ARG R 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    1)
  link_NAG-ASN         : angle       2.19480 (    3)
  link_BETA1-4         : bond        0.00309 (    2)
  link_BETA1-4         : angle       3.41752 (    6)
  hydrogen bonds       : bond        0.03841 (  123)
  hydrogen bonds       : angle       6.29229 (  303)
  SS BOND              : bond        0.00586 (    6)
  SS BOND              : angle       1.45790 (   12)
  covalent geometry    : bond        0.00272 ( 4749)
  covalent geometry    : angle       0.63373 ( 6444)

*********************** 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
  107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.479 
Fit side-chains
REVERT: R  418 ILE cc_start: 0.9156 (tt) cc_final: 0.8935 (tt)
REVERT: R  438 SER cc_start: 0.8068 (p) cc_final: 0.7680 (p)
REVERT: L   25 MET cc_start: 0.6944 (mtp) cc_final: 0.6696 (mtp)
REVERT: H   19 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7661 (mtp85)
  outliers start: 5
  outliers final: 4
  residues processed: 104
  average time/residue: 0.1615
  time to fit residues: 21.6676
Evaluate side-chains
  98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain N residue  124 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 50 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0770
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.159360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.138879 restraints weight = 6554.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141218 restraints weight = 10185.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141510 restraints weight = 5288.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2012

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= 0.137
  Angle     :  0.649  10.649   6465  Z= 0.327
  Chirality :  0.045   0.267    697
  Planarity :  0.005   0.068    819
  Dihedral  :  9.445  69.073    694
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.86 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.14 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.36), residues: 554
  helix: -2.52 (1.15), residues: 19
  sheet: -0.38 (0.39), residues: 199
  loop : -1.93 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 353 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.035   0.002   PHE R 456 
 TYR   0.016   0.001   TYR H  95 
 ARG   0.004   0.001   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       2.47173 (    3)
  link_BETA1-4         : bond        0.00256 (    2)
  link_BETA1-4         : angle       3.43580 (    6)
  hydrogen bonds       : bond        0.03562 (  123)
  hydrogen bonds       : angle       5.99336 (  303)
  SS BOND              : bond        0.00577 (    6)
  SS BOND              : angle       1.41734 (   12)
  covalent geometry    : bond        0.00321 ( 4749)
  covalent geometry    : angle       0.63620 ( 6444)

*********************** 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
  106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.540 
Fit side-chains
REVERT: R  355 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7490 (ttt90)
REVERT: R  418 ILE cc_start: 0.9171 (tt) cc_final: 0.8956 (tt)
REVERT: R  438 SER cc_start: 0.8128 (p) cc_final: 0.7591 (p)
REVERT: H   19 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7562 (mtp85)
REVERT: N  169 GLU cc_start: 0.7472 (mp0) cc_final: 0.7002 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 102
  average time/residue: 0.1561
  time to fit residues: 20.5104
Evaluate side-chains
  101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.176553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149649 restraints weight = 6605.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153691 restraints weight = 7602.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.155710 restraints weight = 4654.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2222

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= 0.145
  Angle     :  0.652   8.695   6465  Z= 0.329
  Chirality :  0.045   0.258    697
  Planarity :  0.005   0.067    819
  Dihedral  :  8.828  62.916    694
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.58 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.94 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.36), residues: 554
  helix: -2.38 (1.12), residues: 19
  sheet: -0.35 (0.39), residues: 200
  loop : -2.00 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 353 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.024   0.001   PHE N  43 
 TYR   0.016   0.001   TYR H  95 
 ARG   0.004   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    1)
  link_NAG-ASN         : angle       2.71184 (    3)
  link_BETA1-4         : bond        0.00301 (    2)
  link_BETA1-4         : angle       3.55204 (    6)
  hydrogen bonds       : bond        0.03591 (  123)
  hydrogen bonds       : angle       5.84136 (  303)
  SS BOND              : bond        0.00548 (    6)
  SS BOND              : angle       1.48002 (   12)
  covalent geometry    : bond        0.00342 ( 4749)
  covalent geometry    : angle       0.63852 ( 6444)

*********************** 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
  105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.511 
Fit side-chains
REVERT: R  355 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7439 (ttt180)
REVERT: R  438 SER cc_start: 0.7925 (p) cc_final: 0.7377 (p)
REVERT: H   19 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7597 (mtp85)
REVERT: N   58 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7439 (m-80)
REVERT: N  169 GLU cc_start: 0.7538 (mp0) cc_final: 0.7055 (mp0)
  outliers start: 14
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1414
  time to fit residues: 18.7452
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  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
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 N residue   29 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0470
   chunk 30 optimal weight:    0.0770
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
R 437 ASN
R 498 GLN
H   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.177914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151171 restraints weight = 6552.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155614 restraints weight = 7582.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.157393 restraints weight = 4269.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2430

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= 0.121
  Angle     :  0.629   9.210   6465  Z= 0.316
  Chirality :  0.044   0.248    697
  Planarity :  0.005   0.067    819
  Dihedral  :  8.085  55.847    694
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.22 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.14 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.36), residues: 554
  helix: -2.21 (1.15), residues: 19
  sheet: -0.40 (0.39), residues: 205
  loop : -1.92 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 436 
 HIS   0.001   0.000   HIS H  59 
 PHE   0.022   0.001   PHE N  43 
 TYR   0.013   0.001   TYR H  95 
 ARG   0.003   0.000   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       2.83376 (    3)
  link_BETA1-4         : bond        0.00318 (    2)
  link_BETA1-4         : angle       3.63201 (    6)
  hydrogen bonds       : bond        0.03238 (  123)
  hydrogen bonds       : angle       5.65426 (  303)
  SS BOND              : bond        0.00685 (    6)
  SS BOND              : angle       1.57725 (   12)
  covalent geometry    : bond        0.00280 ( 4749)
  covalent geometry    : angle       0.61376 ( 6444)

*********************** 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
  112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.496 
Fit side-chains
REVERT: R  406 GLU cc_start: 0.8625 (pm20) cc_final: 0.8174 (pm20)
REVERT: R  438 SER cc_start: 0.7922 (p) cc_final: 0.7362 (p)
REVERT: L   25 MET cc_start: 0.7377 (mtp) cc_final: 0.7127 (mtp)
REVERT: L   36 TYR cc_start: 0.8858 (m-80) cc_final: 0.8582 (m-80)
REVERT: H   19 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7485 (mtp85)
REVERT: H  121 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5748 (pm20)
REVERT: N   58 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7321 (m-80)
REVERT: N  169 GLU cc_start: 0.7576 (mp0) cc_final: 0.7002 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1424
  time to fit residues: 19.6280
Evaluate side-chains
  106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  437 ASN
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  121 GLN
Chi-restraints excluded: chain N residue   29 THR
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 15 optimal weight:    0.0270
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0170
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
R 437 ASN
R 498 GLN
H   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.160477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136736 restraints weight = 6577.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140025 restraints weight = 8822.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.140651 restraints weight = 5177.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2507

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= 0.133
  Angle     :  0.639   9.400   6465  Z= 0.320
  Chirality :  0.044   0.235    697
  Planarity :  0.005   0.067    819
  Dihedral  :  7.624  50.206    694
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.22 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.36), residues: 554
  helix: -1.00 (1.58), residues: 13
  sheet: -0.41 (0.38), residues: 206
  loop : -1.93 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 436 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.024   0.001   PHE N  43 
 TYR   0.014   0.001   TYR H  95 
 ARG   0.003   0.000   ARG R 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       2.92865 (    3)
  link_BETA1-4         : bond        0.00331 (    2)
  link_BETA1-4         : angle       3.80000 (    6)
  hydrogen bonds       : bond        0.03292 (  123)
  hydrogen bonds       : angle       5.55991 (  303)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       1.46768 (   12)
  covalent geometry    : bond        0.00313 ( 4749)
  covalent geometry    : angle       0.62309 ( 6444)

*********************** 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
  107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.509 
Fit side-chains
REVERT: R  406 GLU cc_start: 0.8464 (pm20) cc_final: 0.8182 (pm20)
REVERT: R  438 SER cc_start: 0.7865 (p) cc_final: 0.7382 (p)
REVERT: H   19 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7491 (mtp85)
REVERT: H  121 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.5659 (pm20)
REVERT: N   58 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7387 (m-80)
REVERT: N  169 GLU cc_start: 0.7483 (mp0) cc_final: 0.6932 (mp0)
  outliers start: 15
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1420
  time to fit residues: 18.7155
Evaluate side-chains
  104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  437 ASN
Chi-restraints excluded: chain R residue  498 GLN
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   29 THR
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 39 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0870
   chunk 52 optimal weight:    0.3980
   chunk 29 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.160262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137027 restraints weight = 6557.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.140229 restraints weight = 8614.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140659 restraints weight = 5029.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2557

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= 0.133
  Angle     :  0.640   9.444   6465  Z= 0.321
  Chirality :  0.044   0.220    697
  Planarity :  0.005   0.067    819
  Dihedral  :  7.196  45.876    694
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.40 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.36), residues: 554
  helix: -0.99 (1.58), residues: 13
  sheet: -0.39 (0.38), residues: 206
  loop : -1.90 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 436 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.024   0.001   PHE N  43 
 TYR   0.014   0.001   TYR H  95 
 ARG   0.003   0.000   ARG R 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       2.99493 (    3)
  link_BETA1-4         : bond        0.00309 (    2)
  link_BETA1-4         : angle       3.92179 (    6)
  hydrogen bonds       : bond        0.03276 (  123)
  hydrogen bonds       : angle       5.52333 (  303)
  SS BOND              : bond        0.00586 (    6)
  SS BOND              : angle       1.38771 (   12)
  covalent geometry    : bond        0.00312 ( 4749)
  covalent geometry    : angle       0.62335 ( 6444)

*********************** 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
  107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.474 
Fit side-chains
REVERT: R  406 GLU cc_start: 0.8600 (pm20) cc_final: 0.8219 (pm20)
REVERT: H  121 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5663 (pm20)
REVERT: N   58 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7446 (m-80)
REVERT: N  169 GLU cc_start: 0.7535 (mp0) cc_final: 0.6963 (mp0)
  outliers start: 19
  outliers final: 14
  residues processed: 98
  average time/residue: 0.1321
  time to fit residues: 17.3864
Evaluate side-chains
  104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  121 GLN
Chi-restraints excluded: chain N residue   29 THR
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  197 ILE
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 29 optimal weight:    0.3980
   chunk 14 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0010
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4586

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.178158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153206 restraints weight = 6590.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156788 restraints weight = 8346.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158509 restraints weight = 5019.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2676

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= 0.122
  Angle     :  0.635   9.363   6465  Z= 0.318
  Chirality :  0.043   0.186    697
  Planarity :  0.005   0.066    819
  Dihedral  :  5.781  45.282    694
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.86 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.36), residues: 554
  helix: -2.13 (1.14), residues: 19
  sheet: -0.25 (0.39), residues: 200
  loop : -1.89 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 436 
 HIS   0.001   0.000   HIS H  59 
 PHE   0.023   0.001   PHE N  43 
 TYR   0.014   0.001   TYR H 102 
 ARG   0.003   0.000   ARG R 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       3.11030 (    3)
  link_BETA1-4         : bond        0.00325 (    2)
  link_BETA1-4         : angle       4.17818 (    6)
  hydrogen bonds       : bond        0.03087 (  123)
  hydrogen bonds       : angle       5.41282 (  303)
  SS BOND              : bond        0.00571 (    6)
  SS BOND              : angle       1.31720 (   12)
  covalent geometry    : bond        0.00284 ( 4749)
  covalent geometry    : angle       0.61659 ( 6444)

*********************** 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
  106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.602 
Fit side-chains
REVERT: R  406 GLU cc_start: 0.8556 (pm20) cc_final: 0.8265 (pm20)
REVERT: R  438 SER cc_start: 0.7710 (p) cc_final: 0.7184 (p)
REVERT: N   58 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7328 (m-80)
REVERT: N  169 GLU cc_start: 0.7468 (mp0) cc_final: 0.6902 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1460
  time to fit residues: 19.0647
Evaluate side-chains
  101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain N residue   29 THR
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 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
R 437 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.159031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137290 restraints weight = 6526.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.139380 restraints weight = 9304.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.139298 restraints weight = 4872.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4758  Z= 0.162
  Angle     :  0.657   8.749   6465  Z= 0.334
  Chirality :  0.044   0.189    697
  Planarity :  0.006   0.081    819
  Dihedral  :  5.242  46.605    694
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.30 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.36), residues: 554
  helix: -2.13 (1.11), residues: 21
  sheet: -0.30 (0.39), residues: 204
  loop : -1.97 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 353 
 HIS   0.002   0.000   HIS H  59 
 PHE   0.026   0.002   PHE N  43 
 TYR   0.017   0.001   TYR H  95 
 ARG   0.004   0.000   ARG R 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00223 (    1)
  link_NAG-ASN         : angle       3.54431 (    3)
  link_BETA1-4         : bond        0.00554 (    2)
  link_BETA1-4         : angle       4.05676 (    6)
  hydrogen bonds       : bond        0.03464 (  123)
  hydrogen bonds       : angle       5.43700 (  303)
  SS BOND              : bond        0.00610 (    6)
  SS BOND              : angle       1.41101 (   12)
  covalent geometry    : bond        0.00385 ( 4749)
  covalent geometry    : angle       0.63892 ( 6444)

********************** 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
  106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.477 
Fit side-chains
REVERT: R  406 GLU cc_start: 0.8546 (pm20) cc_final: 0.8299 (pm20)
REVERT: R  438 SER cc_start: 0.7933 (p) cc_final: 0.7512 (p)
REVERT: H  121 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.5684 (pm20)
REVERT: N   58 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (m-80)
REVERT: N  169 GLU cc_start: 0.7602 (mp0) cc_final: 0.6969 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1402
  time to fit residues: 18.6453
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  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   39 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0000
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5184

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.159887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136062 restraints weight = 6510.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.139336 restraints weight = 9046.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140702 restraints weight = 5082.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4758  Z= 0.128
  Angle     :  0.635   7.933   6465  Z= 0.322
  Chirality :  0.044   0.187    697
  Planarity :  0.006   0.074    819
  Dihedral  :  5.117  45.894    694
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.68 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.36), residues: 554
  helix: -2.69 (0.90), residues: 27
  sheet: -0.22 (0.39), residues: 203
  loop : -1.94 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 436 
 HIS   0.001   0.000   HIS H  59 
 PHE   0.023   0.001   PHE N  43 
 TYR   0.013   0.001   TYR H  95 
 ARG   0.004   0.000   ARG R 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00252 (    1)
  link_NAG-ASN         : angle       4.07481 (    3)
  link_BETA1-4         : bond        0.00470 (    2)
  link_BETA1-4         : angle       3.71529 (    6)
  hydrogen bonds       : bond        0.03122 (  123)
  hydrogen bonds       : angle       5.37453 (  303)
  SS BOND              : bond        0.00581 (    6)
  SS BOND              : angle       1.31682 (   12)
  covalent geometry    : bond        0.00299 ( 4749)
  covalent geometry    : angle       0.61667 ( 6444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2012.98 seconds
wall clock time: 35 minutes 58.92 seconds (2158.92 seconds total)