Starting phenix.real_space_refine
on Sun Apr  5 00:16:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x91_33063/04_2026/7x91_33063.map"
  }
  resolution = 4.3
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2137      2.51       5
     N     560      2.21       5
     O     652      1.98       5
     H    3196      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6559
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 3094
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 11, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 1834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 1834
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1603
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 8, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.20, per 1000 atoms: 0.18
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (85.387, 96.164, 81.242, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     O     652      8.00
     N     560      7.00
     C    2137      6.00
     H    3196      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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 B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 306.4 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 7 sheets defined
      4.7% alpha, 27.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.068A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 5.611A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.615A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.682A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.681A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU H  83 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 60
      removed outlier: 4.148A  pdb=" N   ASN H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   TRP H  50 " --> pdb=" O   ASN H  59 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG H  44 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 5.031A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 106 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)

    87 hydrogen bonds defined for protein.
    207 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: 0.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3193
        1.03 -     1.23: 8
        1.23 -     1.42: 1510
        1.42 -     1.62: 1920
        1.62 -     1.81: 15
  Bond restraints: 6646
  Sorted by residual:
  bond pdb=" N   GLU H   1 "
       pdb=" CA  GLU H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   ASP L   1 "
       pdb=" CA  ASP L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" N   GLU H   1 "
       pdb=" H   GLU H   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" N   ASP L   1 "
       pdb=" H   ASP L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.19e+00
  ... (remaining 6641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 11620
        1.52 -     3.04: 267
        3.04 -     4.56: 30
        4.56 -     6.08: 0
        6.08 -     7.60: 1
  Bond angle restraints: 11918
  Sorted by residual:
  angle pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     110.70  113.67   -2.97 1.22e+00 6.72e-01 5.91e+00
  angle pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
        pdb=" N   PRO L  96 "
      ideal   model   delta    sigma   weight residual
     117.93  120.78   -2.85 1.20e+00 6.94e-01 5.64e+00
  angle pdb=" N   GLY H   8 "
        pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
      ideal   model   delta    sigma   weight residual
     112.34  116.84   -4.50 2.04e+00 2.40e-01 4.88e+00
  angle pdb=" N   GLY A 381 "
        pdb=" CA  GLY A 381 "
        pdb=" C   GLY A 381 "
      ideal   model   delta    sigma   weight residual
     115.08  112.69    2.39 1.19e+00 7.06e-01 4.05e+00
  angle pdb=" CA  CYS L  88 "
        pdb=" CB  CYS L  88 "
        pdb=" SG  CYS L  88 "
      ideal   model   delta    sigma   weight residual
     114.40  118.93   -4.53 2.30e+00 1.89e-01 3.89e+00
  ... (remaining 11913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 2898
       17.76 -    35.53: 265
       35.53 -    53.29: 55
       53.29 -    71.06: 22
       71.06 -    88.82: 6
  Dihedral angle restraints: 3246
    sinusoidal: 1739
      harmonic: 1507
  Sorted by residual:
  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  150.68  -57.68     1      1.00e+01 1.00e-02 4.47e+01
  dihedral pdb=" CA  SER H  75 "
           pdb=" C   SER H  75 "
           pdb=" N   THR H  76 "
           pdb=" CA  THR H  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.03   23.97     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ALA L  92 "
           pdb=" C   ALA L  92 "
           pdb=" N   ASN L  93 "
           pdb=" CA  ASN L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 299
       0.032 -    0.064: 139
       0.064 -    0.096: 43
       0.096 -    0.128: 26
       0.128 -    0.160: 7
  Chirality restraints: 514
  Sorted by residual:
  chirality pdb=" CA  ILE L  39 "
            pdb=" N   ILE L  39 "
            pdb=" C   ILE L  39 "
            pdb=" CB  ILE L  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE L  21 "
            pdb=" N   ILE L  21 "
            pdb=" C   ILE L  21 "
            pdb=" CB  ILE L  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE H  70 "
            pdb=" N   ILE H  70 "
            pdb=" C   ILE H  70 "
            pdb=" CB  ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 511 not shown)

  Planarity restraints: 1010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.020 2.00e-02 2.50e+03   1.30e-02 6.71e+00
        pdb=" CG  TRP H  36 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TRP H  36 "   -0.008 2.00e-02 2.50e+03
        pdb=" HE1 TRP H  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE3 TRP H  36 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP H  36 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ3 TRP H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" HH2 TRP H  36 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H  73 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" CG  ASP H  73 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASP H  73 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP H  73 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L  39 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO L  40 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO L  40 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L  40 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1007 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 357
        2.17 -     2.78: 12569
        2.78 -     3.38: 17088
        3.38 -     3.99: 22024
        3.99 -     4.60: 33342
  Nonbonded interactions: 85380
  Sorted by model distance:
  nonbonded pdb=" O   VAL H  52 "
            pdb="HH21 ARG H  72 "
     model   vdw
     1.559 2.450
  nonbonded pdb="HH21 ARG H  67 "
            pdb=" O   SER H  85 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" OD1 ASP L 106 "
            pdb=" H   ILE L 107 "
     model   vdw
     1.693 2.450
  nonbonded pdb=" OE1 GLU A 340 "
            pdb=" H   GLU A 340 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" OG  SER A 349 "
            pdb=" H   LEU A 452 "
     model   vdw
     1.708 2.450
  ... (remaining 85375 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:             0.260
  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:             0.040
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.650
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3457  Z= 0.143
  Angle     :  0.628   7.597   4715  Z= 0.335
  Chirality :  0.046   0.160    514
  Planarity :  0.003   0.030    609
  Dihedral  : 14.403  88.821   1261
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.38), residues: 421
  helix: -3.86 (0.64), residues: 24
  sheet: -0.91 (0.48), residues: 117
  loop : -2.10 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  72 
 TYR   0.011   0.001   TYR A 453 
 PHE   0.011   0.001   PHE L  99 
 TRP   0.043   0.002   TRP H  36 
 HIS   0.004   0.003   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3450)
  covalent geometry    : angle       0.62557 ( 4699)
  SS BOND              : bond        0.00287 (    5)
  SS BOND              : angle       0.90919 (   10)
  hydrogen bonds       : bond        0.13760 (   87)
  hydrogen bonds       : angle       6.91154 (  207)
  link_BETA1-4         : bond        0.00213 (    1)
  link_BETA1-4         : angle       0.97940 (    3)
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.85756 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7342 (mm-30)
REVERT: H   80 TYR cc_start: 0.8271 (m-80) cc_final: 0.7786 (m-10)
REVERT: L   53 ASN cc_start: 0.8995 (t0) cc_final: 0.8742 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2228
  time to fit residues: 24.1795
Evaluate side-chains
  66 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 474 GLN
A 493 GLN
L  32 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.042315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.031994 restraints weight = 68649.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.033978 restraints weight = 29123.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.035332 restraints weight = 16143.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.036223 restraints weight = 10337.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.036816 restraints weight = 7380.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3457  Z= 0.227
  Angle     :  0.641   7.232   4715  Z= 0.335
  Chirality :  0.044   0.144    514
  Planarity :  0.005   0.056    609
  Dihedral  :  6.285  55.955    511
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.54 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.38), residues: 421
  helix: -3.29 (0.85), residues: 24
  sheet: -1.16 (0.44), residues: 131
  loop : -2.12 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  44 
 TYR   0.014   0.002   TYR A 449 
 PHE   0.016   0.002   PHE A 377 
 TRP   0.010   0.001   TRP H  36 
 HIS   0.002   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 3450)
  covalent geometry    : angle       0.63307 ( 4699)
  SS BOND              : bond        0.01100 (    5)
  SS BOND              : angle       1.86557 (   10)
  hydrogen bonds       : bond        0.04364 (   87)
  hydrogen bonds       : angle       6.67461 (  207)
  link_BETA1-4         : bond        0.00623 (    1)
  link_BETA1-4         : angle       1.49278 (    3)
  link_NAG-ASN         : bond        0.00443 (    1)
  link_NAG-ASN         : angle       2.19381 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8965 (ttt90) cc_final: 0.8659 (mmm-85)
REVERT: A  442 ASP cc_start: 0.8929 (m-30) cc_final: 0.8502 (m-30)
REVERT: A  462 LYS cc_start: 0.9636 (mmpt) cc_final: 0.9299 (mmtm)
REVERT: A  484 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: H   59 ASN cc_start: 0.9099 (m-40) cc_final: 0.8707 (m110)
REVERT: H   71 THR cc_start: 0.8627 (p) cc_final: 0.8383 (p)
REVERT: H   80 TYR cc_start: 0.9393 (m-80) cc_final: 0.8979 (m-10)
REVERT: L   32 ASN cc_start: 0.9243 (m-40) cc_final: 0.8887 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 69
  average time/residue: 0.2193
  time to fit residues: 17.1206
Evaluate side-chains
  60 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    6.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.041881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.031749 restraints weight = 71506.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.033644 restraints weight = 30643.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.034938 restraints weight = 16969.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.035783 restraints weight = 10884.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.036367 restraints weight = 7861.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3457  Z= 0.232
  Angle     :  0.631   6.924   4715  Z= 0.332
  Chirality :  0.043   0.128    514
  Planarity :  0.005   0.053    609
  Dihedral  :  6.321  54.012    511
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.83 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.38), residues: 421
  helix: -2.59 (1.11), residues: 18
  sheet: -1.13 (0.44), residues: 133
  loop : -2.16 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  74 
 TYR   0.025   0.002   TYR A 449 
 PHE   0.021   0.002   PHE L  71 
 TRP   0.005   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3450)
  covalent geometry    : angle       0.62521 ( 4699)
  SS BOND              : bond        0.00486 (    5)
  SS BOND              : angle       1.67390 (   10)
  hydrogen bonds       : bond        0.03952 (   87)
  hydrogen bonds       : angle       6.76380 (  207)
  link_BETA1-4         : bond        0.00789 (    1)
  link_BETA1-4         : angle       1.06788 (    3)
  link_NAG-ASN         : bond        0.00526 (    1)
  link_NAG-ASN         : angle       1.96537 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8949 (ttt90) cc_final: 0.8694 (mmm-85)
REVERT: A  442 ASP cc_start: 0.8840 (m-30) cc_final: 0.8344 (m-30)
REVERT: A  484 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: H   59 ASN cc_start: 0.8984 (m-40) cc_final: 0.8582 (m110)
REVERT: H   71 THR cc_start: 0.8742 (p) cc_final: 0.8419 (p)
REVERT: H   80 TYR cc_start: 0.9417 (m-80) cc_final: 0.8943 (m-10)
REVERT: L   32 ASN cc_start: 0.9351 (m-40) cc_final: 0.9044 (m-40)
REVERT: L   36 TYR cc_start: 0.9582 (m-10) cc_final: 0.9372 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2406
  time to fit residues: 17.3785
Evaluate side-chains
  52 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:   30.0000
   chunk 27 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.040796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.030703 restraints weight = 72544.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.032570 restraints weight = 30817.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.033822 restraints weight = 17128.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.034675 restraints weight = 11063.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.035240 restraints weight = 7986.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3457  Z= 0.193
  Angle     :  0.591   6.686   4715  Z= 0.308
  Chirality :  0.043   0.136    514
  Planarity :  0.005   0.033    609
  Dihedral  :  6.210  54.296    511
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.39), residues: 421
  helix: -2.50 (1.16), residues: 18
  sheet: -0.80 (0.47), residues: 122
  loop : -2.32 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  74 
 TYR   0.018   0.002   TYR A 449 
 PHE   0.016   0.002   PHE A 400 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3450)
  covalent geometry    : angle       0.58771 ( 4699)
  SS BOND              : bond        0.00375 (    5)
  SS BOND              : angle       0.93887 (   10)
  hydrogen bonds       : bond        0.03549 (   87)
  hydrogen bonds       : angle       6.66114 (  207)
  link_BETA1-4         : bond        0.00041 (    1)
  link_BETA1-4         : angle       1.35384 (    3)
  link_NAG-ASN         : bond        0.00395 (    1)
  link_NAG-ASN         : angle       1.84437 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8951 (ttt90) cc_final: 0.8718 (mmm-85)
REVERT: A  484 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8036 (mm-30)
REVERT: H   59 ASN cc_start: 0.9014 (m-40) cc_final: 0.8623 (m110)
REVERT: H   71 THR cc_start: 0.8700 (p) cc_final: 0.8378 (p)
REVERT: H   80 TYR cc_start: 0.9385 (m-80) cc_final: 0.8913 (m-10)
REVERT: L   32 ASN cc_start: 0.9357 (m-40) cc_final: 0.9057 (m-40)
REVERT: L   86 TYR cc_start: 0.9555 (m-10) cc_final: 0.9155 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2465
  time to fit residues: 17.5084
Evaluate side-chains
  48 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    3.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.041012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.030892 restraints weight = 71962.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.032802 restraints weight = 30902.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.034071 restraints weight = 17216.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.034930 restraints weight = 11123.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.035514 restraints weight = 8013.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3457  Z= 0.143
  Angle     :  0.566   6.519   4715  Z= 0.290
  Chirality :  0.044   0.133    514
  Planarity :  0.004   0.031    609
  Dihedral  :  5.952  54.176    511
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.59 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.39), residues: 421
  helix: -2.46 (1.17), residues: 18
  sheet: -0.71 (0.48), residues: 122
  loop : -2.17 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  74 
 TYR   0.019   0.001   TYR A 449 
 PHE   0.019   0.002   PHE L  99 
 TRP   0.005   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3450)
  covalent geometry    : angle       0.56295 ( 4699)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       0.89860 (   10)
  hydrogen bonds       : bond        0.03353 (   87)
  hydrogen bonds       : angle       6.46563 (  207)
  link_BETA1-4         : bond        0.00060 (    1)
  link_BETA1-4         : angle       1.17008 (    3)
  link_NAG-ASN         : bond        0.00229 (    1)
  link_NAG-ASN         : angle       1.63795 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8965 (ttt90) cc_final: 0.8741 (mmm-85)
REVERT: A  484 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: H   59 ASN cc_start: 0.9004 (m-40) cc_final: 0.8729 (m110)
REVERT: H   71 THR cc_start: 0.8707 (p) cc_final: 0.8363 (p)
REVERT: H   80 TYR cc_start: 0.9384 (m-80) cc_final: 0.8933 (m-10)
REVERT: L   32 ASN cc_start: 0.9314 (m-40) cc_final: 0.8992 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2433
  time to fit residues: 17.2680
Evaluate side-chains
  45 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 29 optimal weight:   20.0000
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 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 = 0.3013 r_free = 0.3013 target = 0.041573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.031393 restraints weight = 71085.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.033322 restraints weight = 30214.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.034640 restraints weight = 16682.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.035512 restraints weight = 10697.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.036113 restraints weight = 7715.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3457  Z= 0.122
  Angle     :  0.558   5.894   4715  Z= 0.286
  Chirality :  0.044   0.152    514
  Planarity :  0.005   0.070    609
  Dihedral  :  5.773  54.220    511
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.39), residues: 421
  helix: -2.50 (1.12), residues: 18
  sheet: -0.71 (0.47), residues: 122
  loop : -2.00 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.013   0.001   TYR A 449 
 PHE   0.010   0.001   PHE L  99 
 TRP   0.005   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3450)
  covalent geometry    : angle       0.55396 ( 4699)
  SS BOND              : bond        0.00345 (    5)
  SS BOND              : angle       1.32466 (   10)
  hydrogen bonds       : bond        0.03150 (   87)
  hydrogen bonds       : angle       6.43948 (  207)
  link_BETA1-4         : bond        0.00161 (    1)
  link_BETA1-4         : angle       1.16416 (    3)
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       1.44240 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8036 (mm-30)
REVERT: H   59 ASN cc_start: 0.8958 (m-40) cc_final: 0.8719 (m110)
REVERT: H   80 TYR cc_start: 0.9364 (m-80) cc_final: 0.9116 (m-10)
REVERT: L   32 ASN cc_start: 0.9292 (m-40) cc_final: 0.8964 (m-40)
REVERT: L   86 TYR cc_start: 0.9616 (m-10) cc_final: 0.9034 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2551
  time to fit residues: 17.9806
Evaluate side-chains
  51 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 10 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.042139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.031864 restraints weight = 68762.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.033809 restraints weight = 29426.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.035155 restraints weight = 16337.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036053 restraints weight = 10491.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.036666 restraints weight = 7504.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3457  Z= 0.094
  Angle     :  0.542   5.394   4715  Z= 0.274
  Chirality :  0.045   0.165    514
  Planarity :  0.004   0.035    609
  Dihedral  :  5.555  54.126    511
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.40), residues: 421
  helix: -2.54 (1.05), residues: 18
  sheet: -0.68 (0.48), residues: 116
  loop : -1.66 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  18 
 TYR   0.011   0.001   TYR H  80 
 PHE   0.011   0.001   PHE A 377 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3450)
  covalent geometry    : angle       0.53960 ( 4699)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       1.02933 (   10)
  hydrogen bonds       : bond        0.02983 (   87)
  hydrogen bonds       : angle       6.21680 (  207)
  link_BETA1-4         : bond        0.00179 (    1)
  link_BETA1-4         : angle       1.06793 (    3)
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       1.14557 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 TYR cc_start: 0.8947 (p90) cc_final: 0.8571 (p90)
REVERT: A  484 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7982 (mm-30)
REVERT: H   59 ASN cc_start: 0.8925 (m-40) cc_final: 0.8668 (m110)
REVERT: H   71 THR cc_start: 0.8752 (p) cc_final: 0.8430 (p)
REVERT: H   80 TYR cc_start: 0.9360 (m-80) cc_final: 0.8931 (m-10)
REVERT: L   32 ASN cc_start: 0.9223 (m-40) cc_final: 0.8881 (m-40)
REVERT: L   86 TYR cc_start: 0.9586 (m-10) cc_final: 0.8996 (m-10)
REVERT: L   98 THR cc_start: 0.9399 (t) cc_final: 0.9152 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2351
  time to fit residues: 16.8423
Evaluate side-chains
  53 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.041021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.030939 restraints weight = 72439.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.032825 restraints weight = 31039.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.034115 restraints weight = 17278.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.034998 restraints weight = 11130.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.035588 restraints weight = 7970.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3457  Z= 0.166
  Angle     :  0.560   5.329   4715  Z= 0.287
  Chirality :  0.043   0.148    514
  Planarity :  0.004   0.034    609
  Dihedral  :  5.648  53.414    511
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.39), residues: 421
  helix: -2.27 (1.14), residues: 19
  sheet: -0.62 (0.47), residues: 126
  loop : -1.87 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  74 
 TYR   0.012   0.001   TYR H 103 
 PHE   0.010   0.001   PHE L  71 
 TRP   0.004   0.001   TRP A 353 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3450)
  covalent geometry    : angle       0.55703 ( 4699)
  SS BOND              : bond        0.00303 (    5)
  SS BOND              : angle       0.91224 (   10)
  hydrogen bonds       : bond        0.03126 (   87)
  hydrogen bonds       : angle       6.25144 (  207)
  link_BETA1-4         : bond        0.00072 (    1)
  link_BETA1-4         : angle       1.27563 (    3)
  link_NAG-ASN         : bond        0.00366 (    1)
  link_NAG-ASN         : angle       1.33722 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: H   59 ASN cc_start: 0.8981 (m-40) cc_final: 0.8576 (m110)
REVERT: H   80 TYR cc_start: 0.9343 (m-80) cc_final: 0.9113 (m-10)
REVERT: L   32 ASN cc_start: 0.9265 (m-40) cc_final: 0.8935 (m-40)
REVERT: L   98 THR cc_start: 0.9421 (t) cc_final: 0.9194 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2298
  time to fit residues: 15.1869
Evaluate side-chains
  47 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0870
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    4.0166

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.041132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.031263 restraints weight = 74813.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.033199 restraints weight = 32006.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034534 restraints weight = 17746.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.035442 restraints weight = 11249.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.036054 restraints weight = 7950.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3457  Z= 0.151
  Angle     :  0.578   6.734   4715  Z= 0.295
  Chirality :  0.044   0.153    514
  Planarity :  0.005   0.082    609
  Dihedral  :  5.633  53.830    511
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.40), residues: 421
  helix: -2.27 (1.14), residues: 19
  sheet: -0.56 (0.47), residues: 126
  loop : -1.77 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  18 
 TYR   0.020   0.001   TYR A 449 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.005   0.001   TRP H  36 
 HIS   0.001   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3450)
  covalent geometry    : angle       0.57534 ( 4699)
  SS BOND              : bond        0.00297 (    5)
  SS BOND              : angle       0.94805 (   10)
  hydrogen bonds       : bond        0.03092 (   87)
  hydrogen bonds       : angle       6.27268 (  207)
  link_BETA1-4         : bond        0.00039 (    1)
  link_BETA1-4         : angle       1.20121 (    3)
  link_NAG-ASN         : bond        0.00176 (    1)
  link_NAG-ASN         : angle       1.20135 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7918 (mm-30)
REVERT: H   59 ASN cc_start: 0.8987 (m-40) cc_final: 0.8595 (m110)
REVERT: H   80 TYR cc_start: 0.9331 (m-80) cc_final: 0.9105 (m-10)
REVERT: L   32 ASN cc_start: 0.9267 (m-40) cc_final: 0.8943 (m-40)
REVERT: L   98 THR cc_start: 0.9401 (t) cc_final: 0.9164 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2033
  time to fit residues: 13.3193
Evaluate side-chains
  49 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.2990 r_free = 0.2990 target = 0.040653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.030355 restraints weight = 70707.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.032268 restraints weight = 30933.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.033622 restraints weight = 17359.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.034533 restraints weight = 11181.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.035144 restraints weight = 7974.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3457  Z= 0.158
  Angle     :  0.573   6.398   4715  Z= 0.293
  Chirality :  0.043   0.154    514
  Planarity :  0.004   0.033    609
  Dihedral  :  5.625  53.493    511
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.94 (0.40), residues: 421
  helix: -2.18 (1.16), residues: 19
  sheet: -0.42 (0.48), residues: 121
  loop : -1.71 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.016   0.001   TYR A 449 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3450)
  covalent geometry    : angle       0.57057 ( 4699)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       0.94171 (   10)
  hydrogen bonds       : bond        0.03042 (   87)
  hydrogen bonds       : angle       6.28178 (  207)
  link_BETA1-4         : bond        0.00031 (    1)
  link_BETA1-4         : angle       1.21831 (    3)
  link_NAG-ASN         : bond        0.00212 (    1)
  link_NAG-ASN         : angle       1.13056 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7920 (mm-30)
REVERT: H   59 ASN cc_start: 0.8989 (m-40) cc_final: 0.8581 (m110)
REVERT: L   32 ASN cc_start: 0.9243 (m-40) cc_final: 0.8877 (m-40)
REVERT: L   98 THR cc_start: 0.9393 (t) cc_final: 0.9162 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2296
  time to fit residues: 14.9719
Evaluate side-chains
  48 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 38 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   overall best weight:    4.8786

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 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 = 0.2994 r_free = 0.2994 target = 0.040892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.031254 restraints weight = 73647.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.033100 restraints weight = 31950.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.034382 restraints weight = 17806.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035256 restraints weight = 11372.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.035812 restraints weight = 8019.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3457  Z= 0.184
  Angle     :  0.626   9.645   4715  Z= 0.325
  Chirality :  0.044   0.152    514
  Planarity :  0.005   0.065    609
  Dihedral  :  5.744  53.740    511
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.78 (0.41), residues: 421
  helix: -2.16 (1.17), residues: 19
  sheet: -0.45 (0.48), residues: 127
  loop : -1.53 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  18 
 TYR   0.016   0.002   TYR A 449 
 PHE   0.032   0.002   PHE L  73 
 TRP   0.039   0.002   TRP L  35 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3450)
  covalent geometry    : angle       0.61947 ( 4699)
  SS BOND              : bond        0.00865 (    5)
  SS BOND              : angle       1.89735 (   10)
  hydrogen bonds       : bond        0.03351 (   87)
  hydrogen bonds       : angle       6.26206 (  207)
  link_BETA1-4         : bond        0.00275 (    1)
  link_BETA1-4         : angle       1.17808 (    3)
  link_NAG-ASN         : bond        0.00190 (    1)
  link_NAG-ASN         : angle       1.17405 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.97 seconds
wall clock time: 25 minutes 51.25 seconds (1551.25 seconds total)