Starting phenix.real_space_refine
on Sun Apr 27 00:55:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1m_44084/04_2025/9b1m_44084.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2582      2.51       5
     N     667      2.21       5
     O     682      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3961
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3938
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 515, 3922
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
      Conformer: "B"
        Number of residues, atoms: 515, 3922
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          bond proxies already assigned to first conformer: 4002
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'NAG': 1, 'VGL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.24, per 1000 atoms: 1.32
  Number of scatterers: 3961
  At special positions: 0
  Unit cell: (55.814, 87.615, 102.542, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     682      8.00
     N     667      7.00
     C    2582      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A  56 "
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 989.0 milliseconds
  

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  954

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      81.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 3.849A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 37
      removed outlier: 3.625A  pdb=" N   SER A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.821A  pdb=" N   ALA A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.664A  pdb=" N   ASP A  97 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.793A  pdb=" N   TRP A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.691A  pdb=" N   GLY A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 3.591A  pdb=" N   PHE A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 220
      removed outlier: 3.540A  pdb=" N   ALA A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 222
      No H-bonds generated for 'chain 'A' and resid 221 through 222'
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 252
      removed outlier: 4.152A  pdb=" N  APHE A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 264 through 273
      removed outlier: 4.101A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 303
      removed outlier: 3.528A  pdb=" N   GLN A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 4.057A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 311 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
    Processing helix  chain 'A' and resid 320 through 325
    Processing helix  chain 'A' and resid 326 through 329
      removed outlier: 3.789A  pdb=" N   GLU A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 329'
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 4.058A  pdb=" N   PHE A 337 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.659A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 371'
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 3.761A  pdb=" N   GLY A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
    Processing helix  chain 'A' and resid 400 through 419
      removed outlier: 3.632A  pdb=" N   THR A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 453
      removed outlier: 3.672A  pdb=" N   ILE A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.652A  pdb=" N   ILE A 477 " --> pdb=" O   ARG A 473 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 483 through 489
      removed outlier: 3.632A  pdb=" N   VAL A 487 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 4.151A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      Proline residue:  A 501  - end of helix
      removed outlier: 3.629A  pdb=" N   LEU A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88

    260 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1249
        1.35 -     1.47: 967
        1.47 -     1.58: 1800
        1.58 -     1.70: 0
        1.70 -     1.82: 47
  Bond restraints: 4063
  Sorted by residual:
  bond pdb=" N   PHE A   3 "
       pdb=" CA  PHE A   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.27e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" CA  VAL A 264 "
       pdb=" C   VAL A 264 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.011 8.80e-03 1.29e+04 1.51e+00
  bond pdb=" C   MET A 211 "
       pdb=" O   MET A 211 "
    ideal  model  delta    sigma   weight residual
    1.236  1.250 -0.014 1.15e-02 7.56e+03 1.43e+00
  bond pdb=" C   VAL A  26 "
       pdb=" O   VAL A  26 "
    ideal  model  delta    sigma   weight residual
    1.237  1.251 -0.014 1.17e-02 7.31e+03 1.41e+00
  ... (remaining 4058 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 5241
        1.47 -     2.94: 241
        2.94 -     4.40: 48
        4.40 -     5.87: 13
        5.87 -     7.34: 2
  Bond angle restraints: 5545
  Sorted by residual:
  angle pdb=" CA  TYR A 272 "
        pdb=" CB  TYR A 272 "
        pdb=" CG  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     113.90  121.24   -7.34 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" C   LEU A 271 "
        pdb=" N   TYR A 272 "
        pdb=" CA  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     121.58  116.20    5.38 1.95e+00 2.63e-01 7.60e+00
  angle pdb=" C   VAL A 264 "
        pdb=" CA  VAL A 264 "
        pdb=" CB  VAL A 264 "
      ideal   model   delta    sigma   weight residual
     114.35  111.52    2.83 1.06e+00 8.90e-01 7.14e+00
  angle pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
        pdb=" CG  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     113.90  118.62   -4.72 1.80e+00 3.09e-01 6.87e+00
  angle pdb=" C   VAL A 230 "
        pdb=" N   MET A 231 "
        pdb=" CA  MET A 231 "
      ideal   model   delta    sigma   weight residual
     120.31  116.37    3.94 1.52e+00 4.33e-01 6.71e+00
  ... (remaining 5540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 2261
       16.82 -    33.63: 110
       33.63 -    50.45: 26
       50.45 -    67.26: 4
       67.26 -    84.08: 4
  Dihedral angle restraints: 2405
    sinusoidal: 925
      harmonic: 1480
  Sorted by residual:
  dihedral pdb=" CA  PRO A 457 "
           pdb=" C   PRO A 457 "
           pdb=" N   THR A 458 "
           pdb=" CA  THR A 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.59  -23.41     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  GLU A  38 "
           pdb=" C   GLU A  38 "
           pdb=" N   ASN A  39 "
           pdb=" CA  ASN A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  LEU A  54 "
           pdb=" C   LEU A  54 "
           pdb=" N   ASP A  55 "
           pdb=" CA  ASP A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2402 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 417
       0.034 -    0.067: 163
       0.067 -    0.101: 52
       0.101 -    0.134: 17
       0.134 -    0.168: 4
  Chirality restraints: 653
  Sorted by residual:
  chirality pdb=" CA  TYR A 272 "
            pdb=" N   TYR A 272 "
            pdb=" C   TYR A 272 "
            pdb=" CB  TYR A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" CB  ILE A 153 "
            pdb=" CA  ILE A 153 "
            pdb=" CG1 ILE A 153 "
            pdb=" CG2 ILE A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  PRO A 501 "
            pdb=" N   PRO A 501 "
            pdb=" C   PRO A 501 "
            pdb=" CB  PRO A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 650 not shown)

  Planarity restraints: 693
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 272 "   -0.020 2.00e-02 2.50e+03   1.37e-02 3.77e+00
        pdb=" CG  TYR A 272 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 272 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 272 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 272 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 272 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 272 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 272 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 264 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 265 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 265 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 265 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 479 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 480 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 480 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 480 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 690 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 1718
        2.92 -     3.42: 4066
        3.42 -     3.91: 6448
        3.91 -     4.41: 7711
        4.41 -     4.90: 12208
  Nonbonded interactions: 32151
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 239 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" OH  TYR A 451 "
            pdb=" O   PRO A 512 "
     model   vdw
     2.477 3.040
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" OG  SER A 279 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" N   ASP A 290 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     2.528 3.120
  nonbonded pdb=" O   TRP A  30 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.540 3.040
  ... (remaining 32146 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=0.31 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:             3.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:16.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
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      :  0.004   0.037   4066  Z= 0.212
  Angle     :  0.768   7.338   5552  Z= 0.422
  Chirality :  0.043   0.168    653
  Planarity :  0.006   0.055    692
  Dihedral  : 11.395  84.081   1445
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 0.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.34), residues: 517
  helix: -0.24 (0.24), residues: 377
  sheet:  None (None), residues: 0
  loop :  1.24 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 424 
 PHE   0.022   0.002   PHE A 344 
 TYR   0.033   0.002   TYR A 272 
 ARG   0.003   0.001   ARG A 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00829 (    1)
  link_NAG-ASN         : angle       1.36344 (    3)
  hydrogen bonds       : bond        0.11479 (  260)
  hydrogen bonds       : angle       5.56547 (  753)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       2.45378 (    4)
  covalent geometry    : bond        0.00432 ( 4063)
  covalent geometry    : angle       0.76536 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  219 MET cc_start: 0.6324 (mmp) cc_final: 0.6091 (mmp)
REVERT: A  281 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7208 (mtm-85)
REVERT: A  488 HIS cc_start: 0.7581 (m170) cc_final: 0.7346 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 1.5377
  time to fit residues: 112.9593
Evaluate side-chains
  46 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 368 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110111 restraints weight = 7086.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 3.29
r_work: 0.3121 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4066  Z= 0.156
  Angle     :  0.634   8.791   5552  Z= 0.316
  Chirality :  0.041   0.134    653
  Planarity :  0.005   0.040    692
  Dihedral  :  4.728  49.834    574
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.33 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 517
  helix:  0.79 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop :  1.71 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.015   0.002   PHE A 356 
 TYR   0.023   0.002   TYR A 272 
 ARG   0.005   0.000   ARG A 343 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00397 (    1)
  link_NAG-ASN         : angle       0.97773 (    3)
  hydrogen bonds       : bond        0.05801 (  260)
  hydrogen bonds       : angle       4.40028 (  753)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       1.94993 (    4)
  covalent geometry    : bond        0.00349 ( 4063)
  covalent geometry    : angle       0.63162 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7922 (mm)
REVERT: A  281 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7177 (mtm-85)
REVERT: A  459 VAL cc_start: 0.8281 (m) cc_final: 0.8049 (p)
REVERT: A  462 MET cc_start: 0.4870 (OUTLIER) cc_final: 0.4050 (mpt)
REVERT: A  497 TYR cc_start: 0.8650 (m-80) cc_final: 0.8418 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 1.3538
  time to fit residues: 66.0724
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  272 TYR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0570
   chunk 50 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 488 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.108713 restraints weight = 13232.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.42
r_work: 0.3071 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4066  Z= 0.132
  Angle     :  0.592   8.416   5552  Z= 0.285
  Chirality :  0.039   0.135    653
  Planarity :  0.005   0.038    692
  Dihedral  :  4.158  39.898    574
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  :  8.85 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.37), residues: 517
  helix:  1.17 (0.27), residues: 371
  sheet: -1.35 (1.45), residues: 10
  loop :  1.75 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.012   0.002   PHE A 358 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 343 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (    1)
  link_NAG-ASN         : angle       0.97557 (    3)
  hydrogen bonds       : bond        0.04876 (  260)
  hydrogen bonds       : angle       4.10060 (  753)
  SS BOND              : bond        0.00119 (    2)
  SS BOND              : angle       1.72739 (    4)
  covalent geometry    : bond        0.00301 ( 4063)
  covalent geometry    : angle       0.58964 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8771 (t) cc_final: 0.8223 (m)
REVERT: A  219 MET cc_start: 0.6084 (mmp) cc_final: 0.5087 (mtt)
REVERT: A  281 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7415 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7018 (mtt-85)
REVERT: A  462 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4183 (mpt)
  outliers start: 13
  outliers final: 5
  residues processed: 54
  average time/residue: 0.8816
  time to fit residues: 50.0199
Evaluate side-chains
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.106395 restraints weight = 16722.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 4.86
r_work: 0.3026 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4066  Z= 0.146
  Angle     :  0.577   7.163   5552  Z= 0.281
  Chirality :  0.039   0.140    653
  Planarity :  0.005   0.037    692
  Dihedral  :  3.974  34.688    574
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.81 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.37), residues: 517
  helix:  1.34 (0.27), residues: 364
  sheet: -1.82 (1.48), residues: 10
  loop :  1.54 (0.56), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.013   0.002   PHE A 358 
 TYR   0.021   0.002   TYR A 272 
 ARG   0.005   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    1)
  link_NAG-ASN         : angle       1.18807 (    3)
  hydrogen bonds       : bond        0.05058 (  260)
  hydrogen bonds       : angle       4.06678 (  753)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       1.71225 (    4)
  covalent geometry    : bond        0.00344 ( 4063)
  covalent geometry    : angle       0.57487 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8796 (t) cc_final: 0.8237 (m)
REVERT: A  219 MET cc_start: 0.6276 (mmp) cc_final: 0.5190 (mtt)
REVERT: A  281 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7455 (mtm-85)
REVERT: A  462 MET cc_start: 0.5105 (OUTLIER) cc_final: 0.4326 (mpt)
  outliers start: 10
  outliers final: 4
  residues processed: 50
  average time/residue: 0.9326
  time to fit residues: 48.9272
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  305 HIS
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0770
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.108724 restraints weight = 12244.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.28
r_work: 0.3076 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4066  Z= 0.131
  Angle     :  0.576   8.106   5552  Z= 0.277
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.035    692
  Dihedral  :  3.893  33.217    574
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.05 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.37), residues: 517
  helix:  1.61 (0.27), residues: 358
  sheet: -1.85 (1.55), residues: 10
  loop :  1.36 (0.54), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 305 
 PHE   0.012   0.001   PHE A 358 
 TYR   0.011   0.002   TYR A 497 
 ARG   0.005   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    1)
  link_NAG-ASN         : angle       1.13238 (    3)
  hydrogen bonds       : bond        0.04802 (  260)
  hydrogen bonds       : angle       4.00555 (  753)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       1.64480 (    4)
  covalent geometry    : bond        0.00302 ( 4063)
  covalent geometry    : angle       0.57387 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8730 (t) cc_final: 0.8146 (m)
REVERT: A  281 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.7396 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7125 (mtt-85)
REVERT: A  462 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4300 (mpt)
  outliers start: 10
  outliers final: 5
  residues processed: 47
  average time/residue: 1.0453
  time to fit residues: 51.2102
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.160482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.107281 restraints weight = 14427.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 4.60
r_work: 0.3058 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4066  Z= 0.137
  Angle     :  0.558   6.958   5552  Z= 0.270
  Chirality :  0.039   0.138    653
  Planarity :  0.004   0.035    692
  Dihedral  :  3.785  30.676    574
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.53 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.37), residues: 517
  helix:  1.67 (0.27), residues: 354
  sheet: -2.02 (1.55), residues: 10
  loop :  1.42 (0.54), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.005   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00205 (    1)
  link_NAG-ASN         : angle       1.09730 (    3)
  hydrogen bonds       : bond        0.04833 (  260)
  hydrogen bonds       : angle       3.98568 (  753)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       1.63133 (    4)
  covalent geometry    : bond        0.00323 ( 4063)
  covalent geometry    : angle       0.55639 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8735 (t) cc_final: 0.8145 (m)
REVERT: A  281 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.7415 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7206 (mtt-85)
REVERT: A  462 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.4458 (mpt)
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 0.9659
  time to fit residues: 49.5495
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  297 ARG
Chi-restraints excluded: chain A residue  305 HIS
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   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  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111065 restraints weight = 10001.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 4.31
r_work: 0.3064 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4066  Z= 0.128
  Angle     :  0.566   6.975   5552  Z= 0.272
  Chirality :  0.038   0.139    653
  Planarity :  0.004   0.035    692
  Dihedral  :  3.745  29.797    574
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.53 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.37), residues: 517
  helix:  1.71 (0.27), residues: 358
  sheet: -1.92 (1.65), residues: 10
  loop :  1.43 (0.55), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A 305 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    1)
  link_NAG-ASN         : angle       1.06867 (    3)
  hydrogen bonds       : bond        0.04657 (  260)
  hydrogen bonds       : angle       3.96403 (  753)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       1.77635 (    4)
  covalent geometry    : bond        0.00292 ( 4063)
  covalent geometry    : angle       0.56376 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  120 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (t0)
REVERT: A  126 SER cc_start: 0.8702 (t) cc_final: 0.8104 (m)
REVERT: A  281 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7356 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7187 (mtt-85)
REVERT: A  462 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4378 (mpt)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 1.0397
  time to fit residues: 49.9879
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0470
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 419 ASN
A 488 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.163153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110736 restraints weight = 11861.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 4.27
r_work: 0.3109 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4066  Z= 0.116
  Angle     :  0.549   9.110   5552  Z= 0.261
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.622  27.148    574
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.00 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.37), residues: 517
  helix:  1.74 (0.27), residues: 365
  sheet: -1.49 (1.80), residues: 10
  loop :  1.56 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.012   0.001   PHE A 358 
 TYR   0.018   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    1)
  link_NAG-ASN         : angle       1.03068 (    3)
  hydrogen bonds       : bond        0.04349 (  260)
  hydrogen bonds       : angle       3.90854 (  753)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       1.39737 (    4)
  covalent geometry    : bond        0.00260 ( 4063)
  covalent geometry    : angle       0.54744 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.8211 (mm110) cc_final: 0.7956 (mp10)
REVERT: A  120 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7883 (t0)
REVERT: A  126 SER cc_start: 0.8734 (t) cc_final: 0.8133 (m)
REVERT: A  281 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7419 (mtm-85)
REVERT: A  462 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.4447 (mpt)
  outliers start: 9
  outliers final: 5
  residues processed: 48
  average time/residue: 0.8906
  time to fit residues: 45.0328
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  305 HIS
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107868 restraints weight = 13877.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 4.53
r_work: 0.3053 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4066  Z= 0.139
  Angle     :  0.549   8.499   5552  Z= 0.265
  Chirality :  0.038   0.138    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.614  26.515    574
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.24 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.37), residues: 517
  helix:  1.80 (0.27), residues: 358
  sheet: -1.50 (1.81), residues: 10
  loop :  1.48 (0.55), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.014   0.001   PHE A 358 
 TYR   0.016   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    1)
  link_NAG-ASN         : angle       1.09148 (    3)
  hydrogen bonds       : bond        0.04679 (  260)
  hydrogen bonds       : angle       3.93095 (  753)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       1.51708 (    4)
  covalent geometry    : bond        0.00329 ( 4063)
  covalent geometry    : angle       0.54762 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.8230 (mm110) cc_final: 0.7983 (mp10)
REVERT: A  120 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7929 (t0)
REVERT: A  126 SER cc_start: 0.8747 (t) cc_final: 0.8157 (m)
REVERT: A  281 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7445 (mtm-85)
REVERT: A  462 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4514 (mpt)
  outliers start: 9
  outliers final: 3
  residues processed: 46
  average time/residue: 0.9281
  time to fit residues: 44.7622
Evaluate side-chains
  47 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.108938 restraints weight = 15557.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 4.79
r_work: 0.3059 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4066  Z= 0.124
  Angle     :  0.569   8.705   5552  Z= 0.271
  Chirality :  0.038   0.141    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.600  25.593    574
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.48 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.37), residues: 517
  helix:  1.85 (0.27), residues: 359
  sheet: -1.57 (1.74), residues: 10
  loop :  1.46 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.012   0.001   PHE A 358 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00240 (    1)
  link_NAG-ASN         : angle       0.99965 (    3)
  hydrogen bonds       : bond        0.04497 (  260)
  hydrogen bonds       : angle       3.90451 (  753)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       1.42906 (    4)
  covalent geometry    : bond        0.00278 ( 4063)
  covalent geometry    : angle       0.56711 ( 5545)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8083 (tp30)
REVERT: A   90 GLN cc_start: 0.8218 (mm110) cc_final: 0.7978 (mp10)
REVERT: A  120 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7915 (t0)
REVERT: A  126 SER cc_start: 0.8714 (t) cc_final: 0.8118 (m)
REVERT: A  220 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6548 (mt-10)
REVERT: A  281 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7398 (mtm-85)
REVERT: A  462 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4435 (mpt)
  outliers start: 8
  outliers final: 4
  residues processed: 50
  average time/residue: 1.2394
  time to fit residues: 64.2321
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 305 HIS
A 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.161987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110291 restraints weight = 9494.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 3.90
r_work: 0.3101 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4066  Z= 0.133
  Angle     :  0.588   8.973   5552  Z= 0.283
  Chirality :  0.038   0.139    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.610  24.803    574
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.68 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.37), residues: 517
  helix:  1.82 (0.27), residues: 359
  sheet: -1.62 (1.71), residues: 10
  loop :  1.50 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.007   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00217 (    1)
  link_NAG-ASN         : angle       1.04336 (    3)
  hydrogen bonds       : bond        0.04615 (  260)
  hydrogen bonds       : angle       3.93008 (  753)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.44168 (    4)
  covalent geometry    : bond        0.00307 ( 4063)
  covalent geometry    : angle       0.58628 ( 5545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3402.32 seconds
wall clock time: 59 minutes 29.72 seconds (3569.72 seconds total)