Starting phenix.real_space_refine
on Fri Aug 22 20:52:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uwc_42661/08_2025/8uwc_42661.map"
  }
  resolution = 2.27
  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=   0.018
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      16      5.16       5
     C    2459      2.51       5
     N     655      2.21       5
     O     816      1.98       5
     H    3821      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7767
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 7656
          Classifications: {'peptide': 494}
          Link IDs: {'PCIS': 5, 'PTRANS': 22, 'TRANS': 466}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 111
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1, 'water': 97}
          Link IDs: {None: 97}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.88, per 1000 atoms: 0.24
  Number of scatterers: 7767
  At special positions: 0
  Unit cell: (69.372, 84.87, 90.774, 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      16     16.00
     O     816      8.00
     N     655      7.00
     C    2459      6.00
     H    3821      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 263 " - pdb=" SG  CYS A 407 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 501 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1101 " - " ASN A 515 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 346.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  912

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 7 sheets defined
      29.4% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 80
    Processing helix  chain 'A' and resid 109 through 119
      removed outlier: 3.506A  pdb=" N   GLY A 113 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 198 through 206
      removed outlier: 3.916A  pdb=" N   LEU A 202 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 258
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 315 through 328
    Processing helix  chain 'A' and resid 412 through 431
      removed outlier: 4.032A  pdb=" N   ALA A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   SER A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'A' and resid 438 through 449
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.556A  pdb=" N   GLN A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 478
    Processing helix  chain 'A' and resid 499 through 503
      removed outlier: 3.958A  pdb=" N   GLN A 503 " --> pdb=" O   TYR A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 543
      No H-bonds generated for 'chain 'A' and resid 541 through 543'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87
      removed outlier: 4.714A  pdb=" N   TYR A  54 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 12.287A  pdb=" N   VAL A  51 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 11.662A  pdb=" N   PHE A 133 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 10.271A  pdb=" N   GLU A  53 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
      removed outlier: 10.318A  pdb=" N   LYS A 131 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   GLU A  55 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233
      removed outlier: 7.479A  pdb=" N   ILE A 274 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL A 214 " --> pdb=" O   HIS A 273 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   PHE A 275 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL A 216 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   ASN A 305 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA A 215 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   LEU A 304 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   ALA A 335 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   LEU A 306 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 401
    Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 485
    Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490
      removed outlier: 3.737A  pdb=" N   ASP A 533 " --> pdb=" O   MET A 584 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490

    167 hydrogen bonds defined for protein.
    453 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: 1.95

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 3821
        1.04 -     1.23: 392
        1.23 -     1.43: 1283
        1.43 -     1.63: 2234
        1.63 -     1.83: 28
  Bond restraints: 7758
  Sorted by residual:
  bond pdb=" CA  ASN A  91 "
       pdb=" CB  ASN A  91 "
    ideal  model  delta    sigma   weight residual
    1.527  1.485  0.042 1.75e-02 3.27e+03 5.78e+00
  bond pdb=" CB  CYS A 407 "
       pdb=" SG  CYS A 407 "
    ideal  model  delta    sigma   weight residual
    1.808  1.746  0.062 3.30e-02 9.18e+02 3.49e+00
  bond pdb=" CB  CYS A 263 "
       pdb=" SG  CYS A 263 "
    ideal  model  delta    sigma   weight residual
    1.808  1.747  0.061 3.30e-02 9.18e+02 3.47e+00
  bond pdb=" N   THR A  42 "
       pdb=" CA  THR A  42 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" CB  ARG A  90 "
       pdb=" CG  ARG A  90 "
    ideal  model  delta    sigma   weight residual
    1.520  1.569 -0.049 3.00e-02 1.11e+03 2.72e+00
  ... (remaining 7753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 12975
        1.33 -     2.66: 953
        2.66 -     3.99: 71
        3.99 -     5.33: 20
        5.33 -     6.66: 3
  Bond angle restraints: 14022
  Sorted by residual:
  angle pdb=" N   VAL A  45 "
        pdb=" CA  VAL A  45 "
        pdb=" C   VAL A  45 "
      ideal   model   delta    sigma   weight residual
     106.53  110.77   -4.24 1.41e+00 5.03e-01 9.04e+00
  angle pdb=" C   LEU A 298 "
        pdb=" N   LYS A 299 "
        pdb=" CA  LYS A 299 "
      ideal   model   delta    sigma   weight residual
     120.31  124.83   -4.52 1.52e+00 4.33e-01 8.85e+00
  angle pdb=" C   ILE A 123 "
        pdb=" N   LYS A 124 "
        pdb=" CA  LYS A 124 "
      ideal   model   delta    sigma   weight residual
     120.44  124.29   -3.85 1.36e+00 5.41e-01 8.00e+00
  angle pdb=" CA  TYR A 561 "
        pdb=" CB  TYR A 561 "
        pdb=" CG  TYR A 561 "
      ideal   model   delta    sigma   weight residual
     113.90  118.66   -4.76 1.80e+00 3.09e-01 7.00e+00
  angle pdb=" CG  ARG A 408 "
        pdb=" CD  ARG A 408 "
        pdb=" NE  ARG A 408 "
      ideal   model   delta    sigma   weight residual
     112.00  116.81   -4.81 2.20e+00 2.07e-01 4.78e+00
  ... (remaining 14017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3270
       17.96 -    35.92: 268
       35.92 -    53.88: 106
       53.88 -    71.84: 32
       71.84 -    89.80: 10
  Dihedral angle restraints: 3686
    sinusoidal: 2010
      harmonic: 1676
  Sorted by residual:
  dihedral pdb=" CB  CYS A 263 "
           pdb=" SG  CYS A 263 "
           pdb=" SG  CYS A 407 "
           pdb=" CB  CYS A 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.98  -67.98     1      1.00e+01 1.00e-02 6.00e+01
  dihedral pdb=" CA  SER A 550 "
           pdb=" C   SER A 550 "
           pdb=" N   TYR A 551 "
           pdb=" CA  TYR A 551 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.57  -19.43     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ARG A 527 "
           pdb=" C   ARG A 527 "
           pdb=" N   ILE A 528 "
           pdb=" CA  ILE A 528 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.63   19.37     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 3683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 307
       0.034 -    0.069: 167
       0.069 -    0.103: 87
       0.103 -    0.137: 40
       0.137 -    0.172: 3
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CA  ILE A 528 "
            pdb=" N   ILE A 528 "
            pdb=" C   ILE A 528 "
            pdb=" CB  ILE A 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.36e-01
  chirality pdb=" CB  THR A 286 "
            pdb=" CA  THR A 286 "
            pdb=" OG1 THR A 286 "
            pdb=" CG2 THR A 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  ILE A 106 "
            pdb=" N   ILE A 106 "
            pdb=" C   ILE A 106 "
            pdb=" CB  ILE A 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 601 not shown)

  Planarity restraints: 1146
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  56 "   -0.023 2.00e-02 2.50e+03   1.07e-02 3.44e+00
        pdb=" CG  TYR A  56 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  56 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  56 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD1 TYR A  56 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 TYR A  56 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR A  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 TYR A  56 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 575 "    0.024 2.00e-02 2.50e+03   8.75e-03 3.06e+00
        pdb=" CG  TRP A 575 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 575 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 575 "   -0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 575 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 575 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 575 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 575 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 575 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 575 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 575 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 575 "    0.001 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 575 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 575 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 575 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 575 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 237 "    0.018 2.00e-02 2.50e+03   7.91e-03 2.50e+00
        pdb=" CG  TRP A 237 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 237 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 237 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 237 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 237 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 237 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 237 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 237 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 237 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 237 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 237 "    0.002 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 237 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 237 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 237 "    0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 237 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1143 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 177
        2.08 -     2.71: 13013
        2.71 -     3.34: 23457
        3.34 -     3.97: 31647
        3.97 -     4.60: 48559
  Nonbonded interactions: 116853
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS A 225 "
            pdb=" O   GLY A 402 "
     model   vdw
     1.446 2.450
  nonbonded pdb="HH22 ARG A 134 "
            pdb=" OD1 ASP A 218 "
     model   vdw
     1.477 2.450
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" H   ARG A 470 "
     model   vdw
     1.563 2.450
  nonbonded pdb=" O   ALA A 194 "
            pdb=" H   ALA A 199 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" HH  TYR A  56 "
            pdb=" OE1 GLN A 110 "
     model   vdw
     1.611 2.450
  ... (remaining 116848 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.270
  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:             0.060
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.220
  Find NCS groups from input model:        0.030
  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:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062   3940  Z= 0.362
  Angle     :  0.891   6.657   5355  Z= 0.499
  Chirality :  0.054   0.172    604
  Planarity :  0.005   0.033    682
  Dihedral  : 15.703  89.798   1441
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.59 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.36), residues: 484
  helix: -0.50 (0.43), residues: 121
  sheet: -0.41 (0.50), residues: 102
  loop : -1.62 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  90 
 TYR   0.028   0.004   TYR A  56 
 PHE   0.015   0.003   PHE A 228 
 TRP   0.024   0.004   TRP A 575 
 HIS   0.007   0.002   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00759 ( 3937)
  covalent geometry    : angle       0.88222 ( 5348)
  SS BOND              : bond        0.01143 (    2)
  SS BOND              : angle       2.38065 (    4)
  hydrogen bonds       : bond        0.19356 (  151)
  hydrogen bonds       : angle       9.39841 (  453)
  link_NAG-ASN         : bond        0.00602 (    1)
  link_NAG-ASN         : angle       4.65761 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 63
  average time/residue: 1.1337
  time to fit residues: 74.1604
Evaluate side-chains
  48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  195 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0870
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 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 = 0.4207 r_free = 0.4207 target = 0.145500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.129854 restraints weight = 19389.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 2.43
r_work: 0.3882 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3775 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3940  Z= 0.150
  Angle     :  0.597   4.439   5355  Z= 0.316
  Chirality :  0.048   0.153    604
  Planarity :  0.004   0.031    682
  Dihedral  :  7.753  59.178    558
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.22 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.38), residues: 484
  helix:  0.66 (0.47), residues: 125
  sheet: -0.50 (0.47), residues: 117
  loop : -1.30 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 408 
 TYR   0.016   0.001   TYR A  63 
 PHE   0.009   0.001   PHE A 293 
 TRP   0.011   0.001   TRP A 237 
 HIS   0.006   0.002   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3937)
  covalent geometry    : angle       0.59448 ( 5348)
  SS BOND              : bond        0.00676 (    2)
  SS BOND              : angle       0.98987 (    4)
  hydrogen bonds       : bond        0.04535 (  151)
  hydrogen bonds       : angle       6.34325 (  453)
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       2.32302 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 MET cc_start: 0.6985 (ptm) cc_final: 0.6671 (ptm)
  outliers start: 15
  outliers final: 4
  residues processed: 62
  average time/residue: 1.2189
  time to fit residues: 78.1445
Evaluate side-chains
  47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  307 SER
Chi-restraints excluded: chain A residue  459 PHE
Chi-restraints excluded: chain A residue  469 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0170
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4175 r_free = 0.4175 target = 0.143423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.128859 restraints weight = 19510.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 2.32
r_work: 0.3872 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3940  Z= 0.165
  Angle     :  0.581   5.037   5355  Z= 0.303
  Chirality :  0.048   0.143    604
  Planarity :  0.004   0.033    682
  Dihedral  :  6.685  59.169    552
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.86 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.38), residues: 484
  helix:  0.94 (0.47), residues: 125
  sheet: -0.20 (0.48), residues: 111
  loop : -1.32 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 408 
 TYR   0.011   0.002   TYR A  63 
 PHE   0.010   0.001   PHE A 549 
 TRP   0.009   0.001   TRP A 575 
 HIS   0.007   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3937)
  covalent geometry    : angle       0.57861 ( 5348)
  SS BOND              : bond        0.00640 (    2)
  SS BOND              : angle       0.94797 (    4)
  hydrogen bonds       : bond        0.04361 (  151)
  hydrogen bonds       : angle       5.96327 (  453)
  link_NAG-ASN         : bond        0.00094 (    1)
  link_NAG-ASN         : angle       2.22931 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7766 (mt)
REVERT: A  580 GLN cc_start: 0.7764 (mt0) cc_final: 0.7508 (mt0)
  outliers start: 10
  outliers final: 3
  residues processed: 56
  average time/residue: 1.3054
  time to fit residues: 75.5221
Evaluate side-chains
  48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  469 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.143989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.129654 restraints weight = 19622.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.30
r_work: 0.3889 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3940  Z= 0.127
  Angle     :  0.548   6.106   5355  Z= 0.282
  Chirality :  0.047   0.141    604
  Planarity :  0.004   0.041    682
  Dihedral  :  5.888  58.737    552
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.33 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.38), residues: 484
  helix:  1.15 (0.47), residues: 125
  sheet: -0.24 (0.48), residues: 111
  loop : -1.17 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.010   0.001   TYR A  63 
 PHE   0.007   0.001   PHE A 549 
 TRP   0.009   0.001   TRP A 237 
 HIS   0.007   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3937)
  covalent geometry    : angle       0.54641 ( 5348)
  SS BOND              : bond        0.00583 (    2)
  SS BOND              : angle       0.84163 (    4)
  hydrogen bonds       : bond        0.03780 (  151)
  hydrogen bonds       : angle       5.62298 (  453)
  link_NAG-ASN         : bond        0.00217 (    1)
  link_NAG-ASN         : angle       1.75917 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 54
  average time/residue: 1.0056
  time to fit residues: 56.7587
Evaluate side-chains
  47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 39 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4183 r_free = 0.4183 target = 0.143798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.129218 restraints weight = 19529.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 2.33
r_work: 0.3882 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3940  Z= 0.139
  Angle     :  0.560   7.858   5355  Z= 0.284
  Chirality :  0.047   0.139    604
  Planarity :  0.004   0.034    682
  Dihedral  :  5.571  58.588    552
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.10 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.38), residues: 484
  helix:  1.25 (0.47), residues: 125
  sheet: -0.33 (0.44), residues: 121
  loop : -1.10 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.008   0.001   TYR A  63 
 PHE   0.007   0.001   PHE A 549 
 TRP   0.009   0.001   TRP A 237 
 HIS   0.007   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3937)
  covalent geometry    : angle       0.55779 ( 5348)
  SS BOND              : bond        0.00651 (    2)
  SS BOND              : angle       0.83282 (    4)
  hydrogen bonds       : bond        0.03751 (  151)
  hydrogen bonds       : angle       5.50286 (  453)
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       1.92954 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 6
  residues processed: 54
  average time/residue: 1.0471
  time to fit residues: 58.9787
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4175 r_free = 0.4175 target = 0.142990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.128218 restraints weight = 19774.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.35
r_work: 0.3868 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3765 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3940  Z= 0.154
  Angle     :  0.582   8.758   5355  Z= 0.294
  Chirality :  0.047   0.140    604
  Planarity :  0.004   0.034    682
  Dihedral  :  5.549  58.777    552
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.10 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.39), residues: 484
  helix:  1.26 (0.47), residues: 125
  sheet: -0.34 (0.45), residues: 121
  loop : -1.04 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.007   0.001   TYR A  63 
 PHE   0.008   0.001   PHE A 549 
 TRP   0.009   0.001   TRP A 237 
 HIS   0.008   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3937)
  covalent geometry    : angle       0.57969 ( 5348)
  SS BOND              : bond        0.00613 (    2)
  SS BOND              : angle       0.93137 (    4)
  hydrogen bonds       : bond        0.03838 (  151)
  hydrogen bonds       : angle       5.50890 (  453)
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.97290 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7399 (ptt) cc_final: 0.7187 (ptt)
REVERT: A  580 GLN cc_start: 0.7636 (mt0) cc_final: 0.7112 (mt0)
  outliers start: 10
  outliers final: 6
  residues processed: 51
  average time/residue: 0.9310
  time to fit residues: 49.8156
Evaluate side-chains
  46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4165 r_free = 0.4165 target = 0.142118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.127190 restraints weight = 19769.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.37
r_work: 0.3851 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3746 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3940  Z= 0.188
  Angle     :  0.608   9.885   5355  Z= 0.309
  Chirality :  0.048   0.147    604
  Planarity :  0.004   0.034    682
  Dihedral  :  5.723  59.140    552
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.38 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.38), residues: 484
  helix:  1.13 (0.46), residues: 125
  sheet: -0.44 (0.45), residues: 121
  loop : -1.09 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.008   0.002   TYR A  56 
 PHE   0.010   0.001   PHE A 549 
 TRP   0.009   0.002   TRP A 237 
 HIS   0.008   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3937)
  covalent geometry    : angle       0.60570 ( 5348)
  SS BOND              : bond        0.00744 (    2)
  SS BOND              : angle       1.12680 (    4)
  hydrogen bonds       : bond        0.04114 (  151)
  hydrogen bonds       : angle       5.61855 (  453)
  link_NAG-ASN         : bond        0.00145 (    1)
  link_NAG-ASN         : angle       2.08082 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 10
  residues processed: 49
  average time/residue: 0.9431
  time to fit residues: 48.3956
Evaluate side-chains
  50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  108 GLU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4173 r_free = 0.4173 target = 0.142770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.128217 restraints weight = 19799.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.34
r_work: 0.3869 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3940  Z= 0.152
  Angle     :  0.587   9.988   5355  Z= 0.296
  Chirality :  0.047   0.139    604
  Planarity :  0.004   0.033    682
  Dihedral  :  5.577  58.848    552
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.62 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.38), residues: 484
  helix:  1.27 (0.47), residues: 125
  sheet: -0.36 (0.46), residues: 119
  loop : -1.03 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.008   0.001   TYR A  63 
 PHE   0.007   0.001   PHE A 549 
 TRP   0.011   0.001   TRP A 237 
 HIS   0.007   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3937)
  covalent geometry    : angle       0.58538 ( 5348)
  SS BOND              : bond        0.00654 (    2)
  SS BOND              : angle       0.89332 (    4)
  hydrogen bonds       : bond        0.03787 (  151)
  hydrogen bonds       : angle       5.48734 (  453)
  link_NAG-ASN         : bond        0.00027 (    1)
  link_NAG-ASN         : angle       1.84903 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 7
  residues processed: 49
  average time/residue: 0.9660
  time to fit residues: 49.5501
Evaluate side-chains
  48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4178 r_free = 0.4178 target = 0.144065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129306 restraints weight = 19620.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.35
r_work: 0.3871 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3940  Z= 0.131
  Angle     :  0.568   9.847   5355  Z= 0.284
  Chirality :  0.046   0.137    604
  Planarity :  0.004   0.033    682
  Dihedral  :  5.452  58.740    552
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.86 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.39), residues: 484
  helix:  1.39 (0.47), residues: 125
  sheet: -0.33 (0.46), residues: 119
  loop : -0.91 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.007   0.001   TYR A  63 
 PHE   0.006   0.001   PHE A 549 
 TRP   0.010   0.001   TRP A 237 
 HIS   0.006   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3937)
  covalent geometry    : angle       0.56696 ( 5348)
  SS BOND              : bond        0.00562 (    2)
  SS BOND              : angle       0.69814 (    4)
  hydrogen bonds       : bond        0.03559 (  151)
  hydrogen bonds       : angle       5.35983 (  453)
  link_NAG-ASN         : bond        0.00015 (    1)
  link_NAG-ASN         : angle       1.76137 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 51
  average time/residue: 0.9434
  time to fit residues: 50.3911
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.143371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.128434 restraints weight = 19711.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.38
r_work: 0.3872 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3940  Z= 0.127
  Angle     :  0.568   9.765   5355  Z= 0.285
  Chirality :  0.046   0.138    604
  Planarity :  0.004   0.032    682
  Dihedral  :  5.404  58.839    552
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 19.86 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.39), residues: 484
  helix:  1.42 (0.47), residues: 125
  sheet: -0.28 (0.47), residues: 119
  loop : -0.84 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.009   0.001   TYR A 496 
 PHE   0.007   0.001   PHE A 549 
 TRP   0.010   0.001   TRP A 237 
 HIS   0.006   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3937)
  covalent geometry    : angle       0.56709 ( 5348)
  SS BOND              : bond        0.00536 (    2)
  SS BOND              : angle       0.65327 (    4)
  hydrogen bonds       : bond        0.03505 (  151)
  hydrogen bonds       : angle       5.31491 (  453)
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.67850 (    3)

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  510 MET cc_start: 0.7710 (mpp) cc_final: 0.7470 (mpp)
  outliers start: 7
  outliers final: 7
  residues processed: 47
  average time/residue: 0.8969
  time to fit residues: 44.1251
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 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 = 0.4156 r_free = 0.4156 target = 0.141626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.127000 restraints weight = 19680.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.34
r_work: 0.3850 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3748 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3940  Z= 0.187
  Angle     :  0.598   9.263   5355  Z= 0.308
  Chirality :  0.047   0.147    604
  Planarity :  0.004   0.033    682
  Dihedral  :  5.651  59.572    552
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.38 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.39), residues: 484
  helix:  1.23 (0.47), residues: 125
  sheet: -0.32 (0.47), residues: 119
  loop : -1.01 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.010   0.002   TYR A  63 
 PHE   0.009   0.002   PHE A 549 
 TRP   0.009   0.002   TRP A 237 
 HIS   0.007   0.001   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3937)
  covalent geometry    : angle       0.59600 ( 5348)
  SS BOND              : bond        0.00736 (    2)
  SS BOND              : angle       1.11594 (    4)
  hydrogen bonds       : bond        0.04037 (  151)
  hydrogen bonds       : angle       5.49381 (  453)
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       1.91688 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4165.07 seconds
wall clock time: 71 minutes 29.43 seconds (4289.43 seconds total)