Starting phenix.real_space_refine
on Tue Aug  4 13:26:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uhh_64164/08_2026/9uhh_64164.cif"
  }
  resolution = 4.05
  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=   0.050
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      17      5.16       5
     C    2076      2.51       5
     N     549      2.21       5
     O     641      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3283
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 894
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
    Chain: "B"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 830
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1545
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.11, per 1000 atoms: 0.34
  Number of scatterers: 3283
  At special positions: 0
  Unit cell: (61.36, 81.12, 95.68, 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      17     16.00
     O     641      8.00
     N     549      7.00
     C    2076      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C1001 " - " ASN C 343 "
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 145.7 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 7 sheets defined
      8.1% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 90
      removed outlier: 3.576A  pdb=" N   THR A  90 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.566A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.932A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER A  25 " --> pdb=" O   GLN A   3 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A   5 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A   7 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU A  78 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 5.452A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 116 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A  96 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   MET A  34 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   VAL A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.669A  pdb=" N   TYR B  87 " --> pdb=" O   TYR B  36 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN B  37 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS B  45 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 21
      removed outlier: 3.877A  pdb=" N   VAL B  19 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B  75 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER B  65 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR B  74 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.621A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   TYR C 380 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 453
      removed outlier: 3.630A  pdb=" N   TYR C 453 " --> pdb=" O   GLN C 493 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN C 493 " --> pdb=" O   TYR C 453 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    72 hydrogen bonds defined for protein.
    171 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: 0.29

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1058
        1.34 -     1.46: 879
        1.46 -     1.59: 1401
        1.59 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 3360
  Sorted by residual:
  bond pdb=" CB  GLU B  81 "
       pdb=" CG  GLU B  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CG  ARG C 408 "
       pdb=" CD  ARG C 408 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 9.02e-01
  bond pdb=" CB  GLN B   3 "
       pdb=" CG  GLN B   3 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.45e-01
  bond pdb=" C   SER B   7 "
       pdb=" N   PRO B   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.88e-01
  bond pdb=" C   SER B  65 "
       pdb=" N   GLY B  66 "
    ideal  model  delta    sigma   weight residual
    1.328  1.316  0.011 1.31e-02 5.83e+03 7.61e-01
  ... (remaining 3355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 4467
        1.79 -     3.58: 81
        3.58 -     5.38: 13
        5.38 -     7.17: 1
        7.17 -     8.96: 1
  Bond angle restraints: 4563
  Sorted by residual:
  angle pdb=" CA  GLU B  81 "
        pdb=" CB  GLU B  81 "
        pdb=" CG  GLU B  81 "
      ideal   model   delta    sigma   weight residual
     114.10  119.48   -5.38 2.00e+00 2.50e-01 7.23e+00
  angle pdb=" CB  GLU B  81 "
        pdb=" CG  GLU B  81 "
        pdb=" CD  GLU B  81 "
      ideal   model   delta    sigma   weight residual
     112.60  117.04   -4.44 1.70e+00 3.46e-01 6.81e+00
  angle pdb=" CA  LEU A  45 "
        pdb=" CB  LEU A  45 "
        pdb=" CG  LEU A  45 "
      ideal   model   delta    sigma   weight residual
     116.30  125.26   -8.96 3.50e+00 8.16e-02 6.55e+00
  angle pdb=" N   SER B   7 "
        pdb=" CA  SER B   7 "
        pdb=" C   SER B   7 "
      ideal   model   delta    sigma   weight residual
     109.81  114.50   -4.69 2.21e+00 2.05e-01 4.51e+00
  angle pdb=" CB  GLN B   3 "
        pdb=" CG  GLN B   3 "
        pdb=" CD  GLN B   3 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -3.54 1.70e+00 3.46e-01 4.34e+00
  ... (remaining 4558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 1748
       15.04 -    30.08: 179
       30.08 -    45.12: 54
       45.12 -    60.16: 12
       60.16 -    75.19: 5
  Dihedral angle restraints: 1998
    sinusoidal: 786
      harmonic: 1212
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.73   41.27     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.39  -32.39     1      1.00e+01 1.00e-02 1.49e+01
  dihedral pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  95 "
           pdb=" CB  CYS A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.83   28.17     1      1.00e+01 1.00e-02 1.14e+01
  ... (remaining 1995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 274
       0.026 -    0.052: 129
       0.052 -    0.078: 49
       0.078 -    0.104: 27
       0.104 -    0.130: 15
  Chirality restraints: 494
  Sorted by residual:
  chirality pdb=" CB  ILE B  29 "
            pdb=" CA  ILE B  29 "
            pdb=" CG1 ILE B  29 "
            pdb=" CG2 ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.77   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  VAL B  58 "
            pdb=" N   VAL B  58 "
            pdb=" C   VAL B  58 "
            pdb=" CB  VAL B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 491 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  71 "   -0.154 9.50e-02 1.11e+02   6.91e-02 3.12e+00
        pdb=" NE  ARG A  71 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  71 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  71 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  71 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  81 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" CD  GLU B  81 "    0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  81 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  81 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  13 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A  14 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  14 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  14 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 1805
        3.00 -     3.48: 3101
        3.48 -     3.95: 5012
        3.95 -     4.43: 5631
        4.43 -     4.90: 9183
  Nonbonded interactions: 24732
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  81 "
            pdb=" OE1 GLU B  81 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" O   SER A  31 "
            pdb=" OD1 ASN A  32 "
     model   vdw
     2.534 3.040
  nonbonded pdb=" O   GLU B  70 "
            pdb=" OE1 GLU B  70 "
     model   vdw
     2.562 3.040
  nonbonded pdb=" N   MET A  34 "
            pdb=" O   MET A  34 "
     model   vdw
     2.642 2.496
  nonbonded pdb=" O   VAL C 503 "
            pdb=" OE1 GLN C 506 "
     model   vdw
     2.643 3.040
  ... (remaining 24727 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:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.330
  Find NCS groups from input model:        0.010
  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:1.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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      :  0.002   0.033   3367  Z= 0.117
  Angle     :  0.608   8.961   4578  Z= 0.315
  Chirality :  0.042   0.130    494
  Planarity :  0.005   0.069    593
  Dihedral  : 13.697  75.195   1214
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.40), residues: 415
  helix: -4.11 (0.59), residues: 26
  sheet: -0.25 (0.50), residues: 112
  loop : -1.12 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 408 
 TYR   0.011   0.001   TYR C 453 
 PHE   0.007   0.001   PHE C 515 
 TRP   0.003   0.001   TRP C 353 
 HIS   0.001   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 3360)
  covalent geometry    : angle       0.60591 /  0.31 ( 4563)
  SS BOND              : bond        0.00404 /  0.20 (    6)
  SS BOND              : angle       1.02943 /  0.47 (   12)
  hydrogen bonds       : bond        0.21592 / 13.43 (   72)
  hydrogen bonds       : angle      11.91830 /  8.15 (  171)
  link_NAG-ASN         : bond        0.00211 /  0.11 (    1)
  link_NAG-ASN         : angle       1.13428 /  0.62 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.9116 (mmm) cc_final: 0.8911 (mmm)
REVERT: A   36 TRP cc_start: 0.8745 (m100) cc_final: 0.8055 (m100)
REVERT: A   46 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7192 (mm-30)
REVERT: A   67 PHE cc_start: 0.8453 (m-10) cc_final: 0.8194 (m-80)
REVERT: C  428 ASP cc_start: 0.7764 (p0) cc_final: 0.5963 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0788
  time to fit residues: 9.1006
Evaluate side-chains
  87 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.0382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.111924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.100970 restraints weight = 7731.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.103443 restraints weight = 4323.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.105067 restraints weight = 2764.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.106110 restraints weight = 1936.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.106896 restraints weight = 1479.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3367  Z= 0.153
  Angle     :  0.586   8.391   4578  Z= 0.301
  Chirality :  0.043   0.133    494
  Planarity :  0.004   0.035    593
  Dihedral  :  4.516  24.148    488
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.40), residues: 415
  helix: -4.23 (0.56), residues: 26
  sheet: -0.01 (0.50), residues: 113
  loop : -1.07 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  18 
 TYR   0.018   0.002   TYR C 369 
 PHE   0.007   0.001   PHE B  98 
 TRP   0.003   0.001   TRP A  36 
 HIS   0.001   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 3360)
  covalent geometry    : angle       0.58264 /  0.30 ( 4563)
  SS BOND              : bond        0.00457 /  0.23 (    6)
  SS BOND              : angle       0.88096 /  0.38 (   12)
  hydrogen bonds       : bond        0.04089 /  2.79 (   72)
  hydrogen bonds       : angle       8.43922 /  5.80 (  171)
  link_NAG-ASN         : bond        0.00188 /  0.10 (    1)
  link_NAG-ASN         : angle       1.99027 /  1.06 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7184 (mm-30)
REVERT: A   67 PHE cc_start: 0.8492 (m-10) cc_final: 0.8259 (m-80)
REVERT: B    3 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7061 (mm-40)
REVERT: C  392 PHE cc_start: 0.8686 (m-80) cc_final: 0.8462 (m-80)
REVERT: C  428 ASP cc_start: 0.7977 (p0) cc_final: 0.6015 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0818
  time to fit residues: 9.3331
Evaluate side-chains
  84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.108646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.097803 restraints weight = 7798.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.100285 restraints weight = 4323.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101929 restraints weight = 2725.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.103036 restraints weight = 1889.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103772 restraints weight = 1413.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3367  Z= 0.204
  Angle     :  0.664  10.061   4578  Z= 0.331
  Chirality :  0.045   0.141    494
  Planarity :  0.004   0.031    593
  Dihedral  :  5.198  29.986    488
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.40), residues: 415
  helix: -4.26 (0.58), residues: 26
  sheet: -0.19 (0.49), residues: 113
  loop : -1.12 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.015   0.002   TYR A  94 
 PHE   0.011   0.001   PHE B  98 
 TRP   0.006   0.001   TRP A  36 
 HIS   0.001   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.20 ( 3360)
  covalent geometry    : angle       0.65876 /  0.33 ( 4563)
  SS BOND              : bond        0.00513 /  0.26 (    6)
  SS BOND              : angle       0.95935 /  0.50 (   12)
  hydrogen bonds       : bond        0.03899 /  2.67 (   72)
  hydrogen bonds       : angle       8.05189 /  5.56 (  171)
  link_NAG-ASN         : bond        0.00234 /  0.12 (    1)
  link_NAG-ASN         : angle       2.83931 /  1.50 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8050 (tp40)
REVERT: A   46 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7249 (mm-30)
REVERT: A   67 PHE cc_start: 0.8713 (m-10) cc_final: 0.8418 (m-10)
REVERT: B    3 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7238 (mm-40)
REVERT: B  102 THR cc_start: 0.8869 (t) cc_final: 0.8636 (t)
REVERT: C  389 ASP cc_start: 0.8380 (t0) cc_final: 0.8179 (t0)
REVERT: C  428 ASP cc_start: 0.8047 (p0) cc_final: 0.6064 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0619
  time to fit residues: 7.5900
Evaluate side-chains
  85 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0040
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.9596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.112411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101976 restraints weight = 7483.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.104337 restraints weight = 4163.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.105922 restraints weight = 2656.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.106989 restraints weight = 1850.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.107738 restraints weight = 1386.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3367  Z= 0.146
  Angle     :  0.606   6.715   4578  Z= 0.312
  Chirality :  0.045   0.141    494
  Planarity :  0.005   0.070    593
  Dihedral  :  4.783  25.051    488
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.40), residues: 415
  helix: -4.40 (0.51), residues: 26
  sheet: -0.33 (0.47), residues: 113
  loop : -1.03 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  71 
 TYR   0.014   0.001   TYR C 453 
 PHE   0.012   0.001   PHE B  98 
 TRP   0.004   0.000   TRP C 353 
 HIS   0.001   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 3360)
  covalent geometry    : angle       0.60173 /  0.31 ( 4563)
  SS BOND              : bond        0.00569 /  0.29 (    6)
  SS BOND              : angle       1.12942 /  0.51 (   12)
  hydrogen bonds       : bond        0.03529 /  2.39 (   72)
  hydrogen bonds       : angle       7.74781 /  5.35 (  171)
  link_NAG-ASN         : bond        0.00198 /  0.10 (    1)
  link_NAG-ASN         : angle       2.21585 /  1.18 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A   34 MET cc_start: 0.9110 (mmm) cc_final: 0.8704 (mmm)
REVERT: A   46 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7167 (mm-30)
REVERT: A   67 PHE cc_start: 0.8623 (m-10) cc_final: 0.8366 (m-10)
REVERT: B   32 TYR cc_start: 0.8047 (m-80) cc_final: 0.7694 (m-10)
REVERT: C  389 ASP cc_start: 0.8278 (t0) cc_final: 0.8065 (t0)
REVERT: C  428 ASP cc_start: 0.8004 (p0) cc_final: 0.5990 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0508
  time to fit residues: 6.2901
Evaluate side-chains
  88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 37 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 GLN
B  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103826 restraints weight = 7441.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.106197 restraints weight = 4253.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.107796 restraints weight = 2743.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.108878 restraints weight = 1929.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109581 restraints weight = 1455.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3367  Z= 0.118
  Angle     :  0.592   7.223   4578  Z= 0.301
  Chirality :  0.043   0.127    494
  Planarity :  0.004   0.031    593
  Dihedral  :  4.456  23.170    488
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.40), residues: 415
  helix: -4.45 (0.50), residues: 26
  sheet: -0.29 (0.48), residues: 113
  loop : -1.04 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.013   0.001   TYR C 449 
 PHE   0.012   0.001   PHE B  98 
 TRP   0.003   0.000   TRP C 353 
 HIS   0.000   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 3360)
  covalent geometry    : angle       0.58829 /  0.30 ( 4563)
  SS BOND              : bond        0.00426 /  0.22 (    6)
  SS BOND              : angle       1.19648 /  0.59 (   12)
  hydrogen bonds       : bond        0.03255 /  2.22 (   72)
  hydrogen bonds       : angle       7.58347 /  5.29 (  171)
  link_NAG-ASN         : bond        0.00185 /  0.10 (    1)
  link_NAG-ASN         : angle       1.77459 /  0.94 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7230 (mm-30)
REVERT: A   66 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8191 (mtp85)
REVERT: B   32 TYR cc_start: 0.7946 (m-80) cc_final: 0.7636 (m-10)
REVERT: B  102 THR cc_start: 0.8775 (t) cc_final: 0.8561 (t)
REVERT: C  389 ASP cc_start: 0.8215 (t0) cc_final: 0.7974 (t0)
REVERT: C  428 ASP cc_start: 0.7951 (p0) cc_final: 0.5997 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0523
  time to fit residues: 6.5917
Evaluate side-chains
  87 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 39 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0010
   chunk 11 optimal weight:    0.2980
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.5590

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.116162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105949 restraints weight = 7517.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.108263 restraints weight = 4299.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.109830 restraints weight = 2770.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110852 restraints weight = 1941.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.111625 restraints weight = 1470.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3367  Z= 0.117
  Angle     :  0.610   6.119   4578  Z= 0.313
  Chirality :  0.044   0.173    494
  Planarity :  0.004   0.033    593
  Dihedral  :  4.535  22.974    488
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.39), residues: 415
  helix: -4.36 (0.52), residues: 26
  sheet: -0.38 (0.48), residues: 115
  loop : -1.02 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  71 
 TYR   0.013   0.001   TYR C 453 
 PHE   0.015   0.002   PHE A  67 
 TRP   0.003   0.000   TRP C 353 
 HIS   0.000   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 3360)
  covalent geometry    : angle       0.60581 /  0.31 ( 4563)
  SS BOND              : bond        0.00453 /  0.23 (    6)
  SS BOND              : angle       1.22729 /  0.66 (   12)
  hydrogen bonds       : bond        0.03332 /  2.26 (   72)
  hydrogen bonds       : angle       7.55675 /  5.20 (  171)
  link_NAG-ASN         : bond        0.00172 /  0.09 (    1)
  link_NAG-ASN         : angle       1.63741 /  0.87 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   34 MET cc_start: 0.9050 (mmm) cc_final: 0.8770 (mmm)
REVERT: A   46 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: B   32 TYR cc_start: 0.7789 (m-80) cc_final: 0.7559 (m-10)
REVERT: C  389 ASP cc_start: 0.8289 (t0) cc_final: 0.8084 (t0)
REVERT: C  428 ASP cc_start: 0.7892 (p0) cc_final: 0.5901 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0688
  time to fit residues: 8.2154
Evaluate side-chains
  79 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0020
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5768

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.105321 restraints weight = 7637.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.107826 restraints weight = 4289.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.109538 restraints weight = 2721.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.110616 restraints weight = 1881.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111450 restraints weight = 1415.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3367  Z= 0.115
  Angle     :  0.607   6.420   4578  Z= 0.308
  Chirality :  0.044   0.160    494
  Planarity :  0.004   0.030    593
  Dihedral  :  4.490  21.074    488
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.39), residues: 415
  helix: -4.38 (0.52), residues: 26
  sheet: -0.44 (0.47), residues: 115
  loop : -0.97 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 408 
 TYR   0.011   0.001   TYR C 453 
 PHE   0.009   0.001   PHE C 392 
 TRP   0.003   0.000   TRP C 353 
 HIS   0.001   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.11 ( 3360)
  covalent geometry    : angle       0.60356 /  0.31 ( 4563)
  SS BOND              : bond        0.00474 /  0.24 (    6)
  SS BOND              : angle       1.11978 /  0.58 (   12)
  hydrogen bonds       : bond        0.03078 /  2.07 (   72)
  hydrogen bonds       : angle       7.39839 /  5.11 (  171)
  link_NAG-ASN         : bond        0.00177 /  0.09 (    1)
  link_NAG-ASN         : angle       1.62656 /  0.87 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   34 MET cc_start: 0.9033 (mmm) cc_final: 0.8714 (mmm)
REVERT: A   36 TRP cc_start: 0.8560 (m100) cc_final: 0.8060 (m100)
REVERT: B   32 TYR cc_start: 0.7876 (m-80) cc_final: 0.7623 (m-10)
REVERT: C  389 ASP cc_start: 0.8360 (t0) cc_final: 0.8147 (t0)
REVERT: C  428 ASP cc_start: 0.7932 (p0) cc_final: 0.5973 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0700
  time to fit residues: 8.2738
Evaluate side-chains
  82 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0370
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0570
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0070
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.3794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.118674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108226 restraints weight = 7576.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.110571 restraints weight = 4416.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.112149 restraints weight = 2878.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.113167 restraints weight = 2033.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.113981 restraints weight = 1554.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3367  Z= 0.106
  Angle     :  0.616   7.988   4578  Z= 0.314
  Chirality :  0.044   0.148    494
  Planarity :  0.004   0.035    593
  Dihedral  :  4.404  18.347    488
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.39), residues: 415
  helix: -4.19 (0.72), residues: 20
  sheet: -0.48 (0.47), residues: 115
  loop : -0.98 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.011   0.001   TYR C 453 
 PHE   0.009   0.001   PHE C 486 
 TRP   0.003   0.001   TRP C 353 
 HIS   0.000   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 3360)
  covalent geometry    : angle       0.61386 /  0.31 ( 4563)
  SS BOND              : bond        0.00447 /  0.22 (    6)
  SS BOND              : angle       1.10288 /  0.57 (   12)
  hydrogen bonds       : bond        0.03005 /  2.03 (   72)
  hydrogen bonds       : angle       7.27560 /  5.00 (  171)
  link_NAG-ASN         : bond        0.00178 /  0.09 (    1)
  link_NAG-ASN         : angle       1.36945 /  0.73 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   34 MET cc_start: 0.9016 (mmm) cc_final: 0.8653 (mmm)
REVERT: A   36 TRP cc_start: 0.8529 (m100) cc_final: 0.8137 (m100)
REVERT: C  428 ASP cc_start: 0.7896 (p0) cc_final: 0.5891 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0536
  time to fit residues: 6.7986
Evaluate side-chains
  88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.116727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.106184 restraints weight = 7652.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108484 restraints weight = 4477.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.110019 restraints weight = 2939.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.110983 restraints weight = 2098.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.111778 restraints weight = 1633.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3367  Z= 0.135
  Angle     :  0.639   9.673   4578  Z= 0.323
  Chirality :  0.044   0.150    494
  Planarity :  0.004   0.031    593
  Dihedral  :  4.610  19.838    488
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.40), residues: 415
  helix: -4.15 (0.76), residues: 20
  sheet: -0.51 (0.47), residues: 109
  loop : -0.97 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.018   0.002   TYR C 380 
 PHE   0.013   0.001   PHE B  98 
 TRP   0.003   0.000   TRP C 353 
 HIS   0.001   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 3360)
  covalent geometry    : angle       0.63551 /  0.32 ( 4563)
  SS BOND              : bond        0.00481 /  0.24 (    6)
  SS BOND              : angle       1.13720 /  0.60 (   12)
  hydrogen bonds       : bond        0.03017 /  2.05 (   72)
  hydrogen bonds       : angle       7.38526 /  5.06 (  171)
  link_NAG-ASN         : bond        0.00170 /  0.09 (    1)
  link_NAG-ASN         : angle       1.83181 /  0.98 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.9046 (mmm) cc_final: 0.8676 (mmm)
REVERT: A   36 TRP cc_start: 0.8508 (m100) cc_final: 0.8123 (m100)
REVERT: C  428 ASP cc_start: 0.7880 (p0) cc_final: 0.5902 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0628
  time to fit residues: 7.3885
Evaluate side-chains
  82 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0060
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.4596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.117819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.107291 restraints weight = 7585.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.109603 restraints weight = 4331.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.111165 restraints weight = 2829.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.112194 restraints weight = 1996.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.113010 restraints weight = 1526.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3367  Z= 0.117
  Angle     :  0.632   7.686   4578  Z= 0.323
  Chirality :  0.044   0.143    494
  Planarity :  0.004   0.034    593
  Dihedral  :  4.485  18.486    488
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.39), residues: 415
  helix: -4.10 (0.79), residues: 20
  sheet: -0.46 (0.46), residues: 115
  loop : -0.97 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  86 
 TYR   0.018   0.001   TYR C 380 
 PHE   0.012   0.001   PHE B  98 
 TRP   0.004   0.000   TRP C 353 
 HIS   0.000   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 3360)
  covalent geometry    : angle       0.62983 /  0.32 ( 4563)
  SS BOND              : bond        0.00440 /  0.22 (    6)
  SS BOND              : angle       1.06262 /  0.55 (   12)
  hydrogen bonds       : bond        0.03024 /  2.04 (   72)
  hydrogen bonds       : angle       7.25974 /  5.00 (  171)
  link_NAG-ASN         : bond        0.00169 /  0.09 (    1)
  link_NAG-ASN         : angle       1.54713 /  0.83 (    3)

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

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.072 
Fit side-chains
REVERT: C  428 ASP cc_start: 0.7723 (p0) cc_final: 0.5841 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0460
  time to fit residues: 5.2919
Evaluate side-chains
  81 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0970
   chunk 11 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0030
   overall best weight:    0.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.118492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.107868 restraints weight = 7672.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.110270 restraints weight = 4345.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111854 restraints weight = 2793.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.112983 restraints weight = 1974.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.113715 restraints weight = 1482.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3367  Z= 0.113
  Angle     :  0.618   7.043   4578  Z= 0.315
  Chirality :  0.043   0.142    494
  Planarity :  0.004   0.032    593
  Dihedral  :  4.302  17.494    488
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.39), residues: 415
  helix: -4.15 (0.76), residues: 20
  sheet: -0.49 (0.46), residues: 114
  loop : -0.95 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  86 
 TYR   0.017   0.001   TYR C 380 
 PHE   0.013   0.001   PHE C 392 
 TRP   0.004   0.001   TRP C 353 
 HIS   0.001   0.000   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.11 ( 3360)
  covalent geometry    : angle       0.61567 /  0.31 ( 4563)
  SS BOND              : bond        0.00414 /  0.21 (    6)
  SS BOND              : angle       0.90378 /  0.45 (   12)
  hydrogen bonds       : bond        0.02913 /  2.01 (   72)
  hydrogen bonds       : angle       7.19062 /  4.95 (  171)
  link_NAG-ASN         : bond        0.00179 /  0.09 (    1)
  link_NAG-ASN         : angle       1.47566 /  0.79 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 716.46 seconds
wall clock time: 12 minutes 59.31 seconds (779.31 seconds total)