Starting phenix.real_space_refine
on Fri May  9 22:06:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1m_44084/05_2025/9b1m_44084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1m_44084/05_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_44084/05_2025/9b1m_44084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1m_44084/05_2025/9b1m_44084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1m_44084/05_2025/9b1m_44084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1m_44084/05_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-5687/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: 5.29, per 1000 atoms: 1.34
  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: 1.04
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.40
  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: 1.06

  Time building geometry restraints manager: 1.31 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:             3.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     17.090
  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:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.560
-------------------------------------------------------------------------------
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  : 0.380 
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: 1.1085
  time to fit residues: 81.5629
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  : 0.412 
-------------------------------------------------------------------------------
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:    0.5980
   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:    0.7180

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.160223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110879 restraints weight = 6780.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.27
r_work: 0.3136 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2063

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= 0.149
  Angle     :  0.624   8.542   5552  Z= 0.309
  Chirality :  0.041   0.131    653
  Planarity :  0.005   0.042    692
  Dihedral  :  4.646  49.139    574
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.09 %
    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:  1.48 (0.36), residues: 517
  helix:  0.86 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop :  1.74 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.014   0.002   PHE A 356 
 TYR   0.022   0.002   TYR A 272 
 ARG   0.004   0.001   ARG A 343 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (    1)
  link_NAG-ASN         : angle       1.01194 (    3)
  hydrogen bonds       : bond        0.05347 (  260)
  hydrogen bonds       : angle       4.31578 (  753)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.85620 (    4)
  covalent geometry    : bond        0.00341 ( 4063)
  covalent geometry    : angle       0.62181 ( 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
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (mm)
REVERT: A  126 SER cc_start: 0.8765 (t) cc_final: 0.8220 (m)
REVERT: A  281 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7313 (mtm-85)
REVERT: A  459 VAL cc_start: 0.8361 (m) cc_final: 0.8129 (p)
REVERT: A  462 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4189 (mpt)
REVERT: A  497 TYR cc_start: 0.8780 (m-80) cc_final: 0.8564 (m-80)
  outliers start: 8
  outliers final: 1
  residues processed: 47
  average time/residue: 1.0326
  time to fit residues: 50.7138
Evaluate side-chains
  48 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  374 ILE
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:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.160074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107805 restraints weight = 12716.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 4.37
r_work: 0.3054 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    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 = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2368

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= 0.141
  Angle     :  0.593   8.229   5552  Z= 0.287
  Chirality :  0.039   0.134    653
  Planarity :  0.005   0.038    692
  Dihedral  :  4.160  39.496    574
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.33 %
    Favored  : 88.28 %
  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:  1.68 (0.37), residues: 517
  helix:  1.11 (0.27), residues: 371
  sheet: -1.28 (1.49), residues: 10
  loop :  1.74 (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   0.013   0.002   PHE A 358 
 TYR   0.022   0.002   TYR A 272 
 ARG   0.005   0.000   ARG A 343 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    1)
  link_NAG-ASN         : angle       1.00673 (    3)
  hydrogen bonds       : bond        0.05126 (  260)
  hydrogen bonds       : angle       4.12766 (  753)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       1.74408 (    4)
  covalent geometry    : bond        0.00329 ( 4063)
  covalent geometry    : angle       0.59085 ( 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
  59 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8834 (t) cc_final: 0.8294 (m)
REVERT: A  219 MET cc_start: 0.6262 (mmp) cc_final: 0.5205 (mtt)
REVERT: A  281 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7476 (mtm-85)
REVERT: A  462 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4284 (mpt)
  outliers start: 10
  outliers final: 3
  residues processed: 53
  average time/residue: 0.8492
  time to fit residues: 47.4528
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
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:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0970
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0040
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.162546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109332 restraints weight = 17748.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 5.00
r_work: 0.3073 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4066  Z= 0.119
  Angle     :  0.552   7.510   5552  Z= 0.264
  Chirality :  0.038   0.142    653
  Planarity :  0.005   0.036    692
  Dihedral  :  3.841  33.312    574
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.74
  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:  2.05 (0.37), residues: 517
  helix:  1.52 (0.27), residues: 365
  sheet: -1.66 (1.48), residues: 10
  loop :  1.49 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.011   0.001   PHE A 358 
 TYR   0.020   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       1.01116 (    3)
  hydrogen bonds       : bond        0.04448 (  260)
  hydrogen bonds       : angle       3.94033 (  753)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       1.53041 (    4)
  covalent geometry    : bond        0.00264 ( 4063)
  covalent geometry    : angle       0.55001 ( 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
  58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8747 (t) cc_final: 0.8177 (m)
REVERT: A  281 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7455 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7124 (mtt-85)
REVERT: A  462 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4253 (mpt)
  outliers start: 10
  outliers final: 4
  residues processed: 51
  average time/residue: 0.9870
  time to fit residues: 52.6764
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
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  462 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.161451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109284 restraints weight = 12453.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 4.31
r_work: 0.3091 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2757

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= 0.130
  Angle     :  0.548   7.550   5552  Z= 0.265
  Chirality :  0.038   0.139    653
  Planarity :  0.004   0.037    692
  Dihedral  :  3.776  31.174    574
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.77 %
    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:  2.21 (0.37), residues: 517
  helix:  1.69 (0.27), residues: 358
  sheet: -1.80 (1.60), residues: 10
  loop :  1.44 (0.55), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 305 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.020   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 343 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    1)
  link_NAG-ASN         : angle       1.12438 (    3)
  hydrogen bonds       : bond        0.04674 (  260)
  hydrogen bonds       : angle       3.95839 (  753)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       1.56001 (    4)
  covalent geometry    : bond        0.00301 ( 4063)
  covalent geometry    : angle       0.54607 ( 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
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8752 (t) cc_final: 0.8164 (m)
REVERT: A  281 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7455 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7131 (mtt-85)
REVERT: A  462 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4293 (mpt)
  outliers start: 9
  outliers final: 4
  residues processed: 47
  average time/residue: 1.0299
  time to fit residues: 50.5956
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  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  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:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0470
   chunk 34 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.161158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108188 restraints weight = 14568.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 4.63
r_work: 0.3051 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2861

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= 0.133
  Angle     :  0.569   8.630   5552  Z= 0.272
  Chirality :  0.038   0.141    653
  Planarity :  0.004   0.036    692
  Dihedral  :  3.719  29.136    574
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 10.77 %
    Favored  : 86.36 %
  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:  2.23 (0.37), residues: 517
  helix:  1.71 (0.27), residues: 358
  sheet: -1.90 (1.63), residues: 10
  loop :  1.44 (0.55), residues: 149

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   0.020   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       1.10137 (    3)
  hydrogen bonds       : bond        0.04695 (  260)
  hydrogen bonds       : angle       3.95397 (  753)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       1.57738 (    4)
  covalent geometry    : bond        0.00311 ( 4063)
  covalent geometry    : angle       0.56699 ( 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
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8760 (t) cc_final: 0.8166 (m)
REVERT: A  219 MET cc_start: 0.6007 (mmp) cc_final: 0.4910 (mtt)
REVERT: A  281 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7464 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7233 (mtt-85)
REVERT: A  462 MET cc_start: 0.5191 (OUTLIER) cc_final: 0.4444 (mpt)
  outliers start: 12
  outliers final: 7
  residues processed: 51
  average time/residue: 0.9125
  time to fit residues: 48.7721
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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  211 MET
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:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   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 = 0.3852 r_free = 0.3852 target = 0.161927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.110495 restraints weight = 10112.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 3.97
r_work: 0.3103 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
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 = 0.40   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: 0.7654
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4066  Z= 0.123
  Angle     :  0.562   7.689   5552  Z= 0.270
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.684  28.370    574
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.72 %
    Favored  : 86.12 %
  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:  1.79 (0.27), residues: 359
  sheet: -1.92 (1.66), residues: 10
  loop :  1.45 (0.56), residues: 148

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   0.012   0.001   PHE A 358 
 TYR   0.021   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       1.03346 (    3)
  hydrogen bonds       : bond        0.04547 (  260)
  hydrogen bonds       : angle       3.92212 (  753)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       1.81688 (    4)
  covalent geometry    : bond        0.00277 ( 4063)
  covalent geometry    : angle       0.56021 ( 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
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  120 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7874 (t0)
REVERT: A  126 SER cc_start: 0.8776 (t) cc_final: 0.8173 (m)
REVERT: A  281 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7468 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7288 (mtt-85)
REVERT: A  462 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4503 (mpt)
  outliers start: 9
  outliers final: 5
  residues processed: 45
  average time/residue: 1.0842
  time to fit residues: 50.9462
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  : 0.413 
-------------------------------------------------------------------------------
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  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:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0670
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.162560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111201 restraints weight = 11890.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 4.22
r_work: 0.3116 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    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 = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4066  Z= 0.116
  Angle     :  0.549   8.888   5552  Z= 0.262
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.577  25.927    574
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  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:  2.49 (0.37), residues: 517
  helix:  1.93 (0.27), residues: 359
  sheet: -1.63 (1.79), residues: 10
  loop :  1.47 (0.56), 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   0.022   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    1)
  link_NAG-ASN         : angle       0.96501 (    3)
  hydrogen bonds       : bond        0.04318 (  260)
  hydrogen bonds       : angle       3.88801 (  753)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       1.38814 (    4)
  covalent geometry    : bond        0.00257 ( 4063)
  covalent geometry    : angle       0.54770 ( 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
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.8230 (mm110) cc_final: 0.7974 (mp10)
REVERT: A  120 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (t0)
REVERT: A  126 SER cc_start: 0.8745 (t) cc_final: 0.8137 (m)
REVERT: A  281 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7452 (mtm-85)
REVERT: A  462 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4493 (mpt)
  outliers start: 8
  outliers final: 6
  residues processed: 45
  average time/residue: 0.9631
  time to fit residues: 45.4345
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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  379 MET
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:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.162156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.109486 restraints weight = 13871.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 4.58
r_work: 0.3072 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3092

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= 0.122
  Angle     :  0.543   8.227   5552  Z= 0.259
  Chirality :  0.038   0.139    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.540  25.355    574
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.72 %
    Favored  : 86.36 %
  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:  2.48 (0.37), residues: 517
  helix:  1.92 (0.27), residues: 359
  sheet: -1.61 (1.79), residues: 10
  loop :  1.46 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.006   0.001   HIS A 305 
 PHE   0.013   0.001   PHE A 358 
 TYR   0.021   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       1.03157 (    3)
  hydrogen bonds       : bond        0.04405 (  260)
  hydrogen bonds       : angle       3.86098 (  753)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       1.40189 (    4)
  covalent geometry    : bond        0.00278 ( 4063)
  covalent geometry    : angle       0.54190 ( 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
  56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8158 (tp30)
REVERT: A   90 GLN cc_start: 0.8213 (mm110) cc_final: 0.7966 (mp10)
REVERT: A  120 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (t0)
REVERT: A  126 SER cc_start: 0.8719 (t) cc_final: 0.8112 (m)
REVERT: A  281 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7409 (mtm-85)
REVERT: A  462 MET cc_start: 0.5162 (OUTLIER) cc_final: 0.4456 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 1.0937
  time to fit residues: 56.9287
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
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  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 49 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.160584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.107649 restraints weight = 15424.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 4.72
r_work: 0.3056 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    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 = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3070

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= 0.140
  Angle     :  0.573   7.566   5552  Z= 0.278
  Chirality :  0.039   0.137    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.608  25.705    574
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.20 %
    Favored  : 85.89 %
  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:  1.84 (0.27), residues: 358
  sheet: -1.66 (1.79), residues: 10
  loop :  1.47 (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   0.013   0.001   PHE A 358 
 TYR   0.020   0.002   TYR A 272 
 ARG   0.006   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00193 (    1)
  link_NAG-ASN         : angle       1.06119 (    3)
  hydrogen bonds       : bond        0.04735 (  260)
  hydrogen bonds       : angle       3.93571 (  753)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       1.46642 (    4)
  covalent geometry    : bond        0.00331 ( 4063)
  covalent geometry    : angle       0.57190 ( 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
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8084 (tp30)
REVERT: A   90 GLN cc_start: 0.8168 (mm110) cc_final: 0.7929 (mp10)
REVERT: A  120 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7890 (t0)
REVERT: A  126 SER cc_start: 0.8709 (t) cc_final: 0.8110 (m)
REVERT: A  281 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7455 (mtm-85)
REVERT: A  462 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4402 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 47
  average time/residue: 1.1709
  time to fit residues: 57.2185
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
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  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:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.161269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.111603 restraints weight = 9484.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 4.45
r_work: 0.3064 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    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 = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3133

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= 0.135
  Angle     :  0.583   8.800   5552  Z= 0.281
  Chirality :  0.039   0.139    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.614  25.943    574
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.20 %
    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:  2.40 (0.37), residues: 517
  helix:  1.86 (0.27), residues: 358
  sheet: -1.71 (1.72), residues: 10
  loop :  1.44 (0.55), residues: 149

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   0.021   0.002   TYR A 272 
 ARG   0.007   0.000   ARG A 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       1.02971 (    3)
  hydrogen bonds       : bond        0.04634 (  260)
  hydrogen bonds       : angle       3.92931 (  753)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       1.42176 (    4)
  covalent geometry    : bond        0.00313 ( 4063)
  covalent geometry    : angle       0.58127 ( 5545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3148.86 seconds
wall clock time: 55 minutes 16.99 seconds (3316.99 seconds total)