Starting phenix.real_space_refine
on Fri May  9 23:48:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jln_61591/05_2025/9jln_61591.cif"
  }
  resolution = 2.84
  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=  -0.001 sd=   0.079
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: 6
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    2898      2.51       5
     N     629      2.21       5
     O     733      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4295
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 521, 4139
          Classifications: {'peptide': 521}
          Link IDs: {'PTRANS': 24, 'TRANS': 496}
    Chain: "A"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 156
          Unusual residues: {' CL': 1, ' NA': 1, 'NAG': 3, 'TAU': 1, 'Y01': 3}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.33, per 1000 atoms: 0.78
  Number of scatterers: 4295
  At special positions: 0
  Unit cell: (75.492, 71.764, 87.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      33     16.00
     Na      1     11.00
     O     733      8.00
     N     629      7.00
     C    2898      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " 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 701 " - " ASN A 163 "
      " NAG A 702 " - " ASN A 179 "
      " NAG A 703 " - " ASN A 190 "
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 529.9 milliseconds
  

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 0 sheets defined
      82.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 59
      removed outlier: 3.756A  pdb=" N   PHE A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 65
      removed outlier: 3.514A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.765A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 6.097A  pdb=" N   LEU A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      Proline residue:  A  93  - end of helix
    Processing helix  chain 'A' and resid 109 through 117
      removed outlier: 4.413A  pdb=" N   TRP A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 121 through 153
      removed outlier: 4.067A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   TYR A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE A 141 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 161
      removed outlier: 3.933A  pdb=" N   HIS A 161 " --> pdb=" O   PRO A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
    Processing helix  chain 'A' and resid 179 through 183
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 217 through 237
      removed outlier: 3.623A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 266
      removed outlier: 4.081A  pdb=" N   PHE A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.916A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.316A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 316
      removed outlier: 3.823A  pdb=" N   ASN A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 356
      removed outlier: 3.920A  pdb=" N   ASP A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 3.836A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 369 through 378
      Proline residue:  A 375  - end of helix
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.550A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   SER A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 423
      removed outlier: 4.194A  pdb=" N   LEU A 422 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 444
      removed outlier: 4.200A  pdb=" N   ILE A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   ILE A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 465 through 482
      removed outlier: 3.773A  pdb=" N   LEU A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 497
    Processing helix  chain 'A' and resid 503 through 510
    Processing helix  chain 'A' and resid 510 through 526
      removed outlier: 3.713A  pdb=" N   VAL A 514 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.786A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567

    267 hydrogen bonds defined for protein.
    777 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: 1.13

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 646
        1.32 -     1.45: 1317
        1.45 -     1.57: 2427
        1.57 -     1.69: 0
        1.69 -     1.82: 47
  Bond restraints: 4437
  Sorted by residual:
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" CAX Y01 A 706 "
       pdb=" OAF Y01 A 706 "
    ideal  model  delta    sigma   weight residual
    1.247  1.308 -0.061 2.00e-02 2.50e+03 9.42e+00
  bond pdb=" CAX Y01 A 708 "
       pdb=" OAF Y01 A 708 "
    ideal  model  delta    sigma   weight residual
    1.247  1.307 -0.060 2.00e-02 2.50e+03 9.02e+00
  bond pdb=" CAX Y01 A 707 "
       pdb=" OAH Y01 A 707 "
    ideal  model  delta    sigma   weight residual
    1.248  1.308 -0.060 2.00e-02 2.50e+03 8.88e+00
  bond pdb=" CAL Y01 A 706 "
       pdb=" CAX Y01 A 706 "
    ideal  model  delta    sigma   weight residual
    1.540  1.501  0.039 2.00e-02 2.50e+03 3.76e+00
  ... (remaining 4432 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 5980
        2.41 -     4.81: 75
        4.81 -     7.21: 9
        7.21 -     9.62: 3
        9.62 -    12.02: 1
  Bond angle restraints: 6068
  Sorted by residual:
  angle pdb=" O1  TAU A 709 "
        pdb=" S   TAU A 709 "
        pdb=" O2  TAU A 709 "
      ideal   model   delta    sigma   weight residual
     113.04  101.02   12.02 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" C   CYS A 556 "
        pdb=" N   VAL A 557 "
        pdb=" CA  VAL A 557 "
      ideal   model   delta    sigma   weight residual
     120.33  122.78   -2.45 8.00e-01 1.56e+00 9.36e+00
  angle pdb=" CA  LEU A 555 "
        pdb=" CB  LEU A 555 "
        pdb=" CG  LEU A 555 "
      ideal   model   delta    sigma   weight residual
     116.30  125.68   -9.38 3.50e+00 8.16e-02 7.19e+00
  angle pdb=" CAL Y01 A 708 "
        pdb=" CAX Y01 A 708 "
        pdb=" OAH Y01 A 708 "
      ideal   model   delta    sigma   weight residual
     115.62  123.15   -7.53 3.00e+00 1.11e-01 6.30e+00
  angle pdb=" CAL Y01 A 706 "
        pdb=" CAX Y01 A 706 "
        pdb=" OAH Y01 A 706 "
      ideal   model   delta    sigma   weight residual
     115.62  123.10   -7.48 3.00e+00 1.11e-01 6.22e+00
  ... (remaining 6063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.87: 2535
       24.87 -    49.75: 120
       49.75 -    74.62: 14
       74.62 -    99.50: 9
       99.50 -   124.37: 6
  Dihedral angle restraints: 2684
    sinusoidal: 1184
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" C2  NAG A 703 "
           pdb=" C1  NAG A 703 "
           pdb=" O5  NAG A 703 "
           pdb=" C5  NAG A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   61.41 -124.37     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" CAT Y01 A 707 "
           pdb=" CAR Y01 A 707 "
           pdb=" CBC Y01 A 707 "
           pdb=" OAW Y01 A 707 "
      ideal   model   delta sinusoidal    sigma   weight residual
     178.96   60.45  118.51     1      3.00e+01 1.11e-03 1.58e+01
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 171 "
           pdb=" CB  CYS A 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.29   33.29     1      1.00e+01 1.00e-02 1.58e+01
  ... (remaining 2681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 437
       0.032 -    0.065: 169
       0.065 -    0.097: 53
       0.097 -    0.129: 22
       0.129 -    0.161: 3
  Chirality restraints: 684
  Sorted by residual:
  chirality pdb=" CBB Y01 A 707 "
            pdb=" CAC Y01 A 707 "
            pdb=" CAO Y01 A 707 "
            pdb=" CBE Y01 A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.41    0.16 2.00e-01 2.50e+01 6.52e-01
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 190 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CBE Y01 A 707 "
            pdb=" CAP Y01 A 707 "
            pdb=" CBB Y01 A 707 "
            pdb=" CBI Y01 A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.43    0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 681 not shown)

  Planarity restraints: 720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  87 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" C   LEU A  87 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LEU A  87 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A  88 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  92 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO A  93 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 478 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.99e+00
        pdb=" C   VAL A 478 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL A 478 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 479 "    0.008 2.00e-02 2.50e+03
  ... (remaining 717 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 625
        2.76 -     3.29: 4243
        3.29 -     3.83: 7070
        3.83 -     4.36: 7781
        4.36 -     4.90: 14146
  Nonbonded interactions: 33865
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  63 "
            pdb=" OD1 ASN A 333 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OG  SER A  90 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OAH Y01 A 707 "
            pdb=" OAH Y01 A 708 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE1 TRP A  65 "
            pdb=" O   PRO A 367 "
     model   vdw
     2.303 3.120
  ... (remaining 33860 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.060
  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:13.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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   0.070   4441  Z= 0.190
  Angle     :  0.657  12.025   6079  Z= 0.320
  Chirality :  0.041   0.161    684
  Planarity :  0.004   0.039    717
  Dihedral  : 16.025 124.369   1733
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  1.28 (0.39), residues: 519
  helix:  1.69 (0.29), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.13 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 470 
 HIS   0.002   0.000   HIS A 164 
 PHE   0.021   0.001   PHE A 338 
 TYR   0.017   0.001   TYR A 489 
 ARG   0.003   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    3)
  link_NAG-ASN         : angle       0.83903 (    9)
  hydrogen bonds       : bond        0.12643 (  267)
  hydrogen bonds       : angle       4.66527 (  777)
  SS BOND              : bond        0.00296 (    1)
  SS BOND              : angle       1.32831 (    2)
  covalent geometry    : bond        0.00378 ( 4437)
  covalent geometry    : angle       0.65624 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.453 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.8697
  time to fit residues: 62.4531
Evaluate side-chains
  55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   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 540 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.175469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.142578 restraints weight = 5287.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.35
r_work: 0.3771 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4441  Z= 0.119
  Angle     :  0.596  11.297   6079  Z= 0.285
  Chirality :  0.041   0.186    684
  Planarity :  0.004   0.037    717
  Dihedral  : 13.118 112.459    842
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.31 %
    Favored  : 90.11 %
  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:  1.29 (0.39), residues: 519
  helix:  1.75 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -1.38 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 164 
 PHE   0.014   0.001   PHE A 338 
 TYR   0.011   0.001   TYR A  69 
 ARG   0.006   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    3)
  link_NAG-ASN         : angle       1.47743 (    9)
  hydrogen bonds       : bond        0.04018 (  267)
  hydrogen bonds       : angle       4.13672 (  777)
  SS BOND              : bond        0.00254 (    1)
  SS BOND              : angle       0.96982 (    2)
  covalent geometry    : bond        0.00260 ( 4437)
  covalent geometry    : angle       0.59376 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7754 (mm)
  outliers start: 7
  outliers final: 2
  residues processed: 62
  average time/residue: 0.8093
  time to fit residues: 53.1553
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.173393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140444 restraints weight = 5349.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.36
r_work: 0.3739 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4441  Z= 0.124
  Angle     :  0.614  10.732   6079  Z= 0.291
  Chirality :  0.042   0.183    684
  Planarity :  0.004   0.039    717
  Dihedral  : 12.382 111.513    842
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.01 %
    Favored  : 86.97 %
  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:  1.30 (0.39), residues: 519
  helix:  1.80 (0.28), residues: 363
  sheet:  None (None), residues: 0
  loop : -1.44 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.016   0.001   PHE A  79 
 TYR   0.014   0.001   TYR A  69 
 ARG   0.007   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    3)
  link_NAG-ASN         : angle       1.40652 (    9)
  hydrogen bonds       : bond        0.03961 (  267)
  hydrogen bonds       : angle       4.12865 (  777)
  SS BOND              : bond        0.00326 (    1)
  SS BOND              : angle       0.96993 (    2)
  covalent geometry    : bond        0.00279 ( 4437)
  covalent geometry    : angle       0.61183 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.5909 (p90)
REVERT: A  133 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7804 (mm)
REVERT: A  380 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6992 (mmp)
  outliers start: 9
  outliers final: 3
  residues processed: 66
  average time/residue: 0.8136
  time to fit residues: 56.7056
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  432 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0670
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.175962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.143018 restraints weight = 5340.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.38
r_work: 0.3755 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4441  Z= 0.113
  Angle     :  0.610  10.603   6079  Z= 0.285
  Chirality :  0.041   0.185    684
  Planarity :  0.004   0.036    717
  Dihedral  : 11.169 109.786    842
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.71 %
    Favored  : 84.72 %
  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:  1.43 (0.38), residues: 519
  helix:  1.90 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.36 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 212 
 PHE   0.013   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A 532 
 ARG   0.008   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    3)
  link_NAG-ASN         : angle       1.37249 (    9)
  hydrogen bonds       : bond        0.03563 (  267)
  hydrogen bonds       : angle       4.07895 (  777)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       1.01528 (    2)
  covalent geometry    : bond        0.00250 ( 4437)
  covalent geometry    : angle       0.60823 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.5709 (p90)
REVERT: A  133 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7789 (mm)
REVERT: A  284 ARG cc_start: 0.8683 (tmt170) cc_final: 0.8423 (tpt90)
  outliers start: 7
  outliers final: 3
  residues processed: 66
  average time/residue: 0.8587
  time to fit residues: 60.2327
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   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 540 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.174347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.141355 restraints weight = 5396.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.38
r_work: 0.3745 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4441  Z= 0.118
  Angle     :  0.613  10.354   6079  Z= 0.288
  Chirality :  0.042   0.186    684
  Planarity :  0.004   0.039    717
  Dihedral  : 10.548 108.742    842
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.16 %
    Favored  : 83.37 %
  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:  1.34 (0.38), residues: 519
  helix:  1.82 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -1.41 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.014   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.001   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    3)
  link_NAG-ASN         : angle       1.39467 (    9)
  hydrogen bonds       : bond        0.03666 (  267)
  hydrogen bonds       : angle       4.12564 (  777)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       1.07375 (    2)
  covalent geometry    : bond        0.00266 ( 4437)
  covalent geometry    : angle       0.61122 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.5792 (p90)
REVERT: A  133 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7814 (mm)
REVERT: A  380 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6924 (mmp)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 0.8137
  time to fit residues: 56.5983
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  523 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.173492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.140654 restraints weight = 5354.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 2.35
r_work: 0.3741 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4441  Z= 0.120
  Angle     :  0.615   9.880   6079  Z= 0.292
  Chirality :  0.043   0.188    684
  Planarity :  0.004   0.040    717
  Dihedral  :  9.961 107.561    842
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.96 %
    Favored  : 81.57 %
  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:  1.34 (0.38), residues: 519
  helix:  1.81 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -1.39 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 164 
 PHE   0.015   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.008   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00178 (    3)
  link_NAG-ASN         : angle       1.43145 (    9)
  hydrogen bonds       : bond        0.03726 (  267)
  hydrogen bonds       : angle       4.12113 (  777)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       1.09735 (    2)
  covalent geometry    : bond        0.00269 ( 4437)
  covalent geometry    : angle       0.61303 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.5869 (p90)
REVERT: A  133 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7831 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 69
  average time/residue: 0.8376
  time to fit residues: 60.8898
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  523 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.173195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140383 restraints weight = 5399.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 2.35
r_work: 0.3735 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4441  Z= 0.119
  Angle     :  0.639  14.970   6079  Z= 0.299
  Chirality :  0.043   0.189    684
  Planarity :  0.004   0.039    717
  Dihedral  :  9.783 106.529    842
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.75 %
    Favored  : 79.78 %
  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:  1.36 (0.38), residues: 519
  helix:  1.82 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -1.38 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.025   0.001   PHE A 434 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.008   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    3)
  link_NAG-ASN         : angle       1.40477 (    9)
  hydrogen bonds       : bond        0.03733 (  267)
  hydrogen bonds       : angle       4.14309 (  777)
  SS BOND              : bond        0.00296 (    1)
  SS BOND              : angle       1.08621 (    2)
  covalent geometry    : bond        0.00272 ( 4437)
  covalent geometry    : angle       0.63733 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.5842 (p90)
REVERT: A  133 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7844 (mm)
  outliers start: 11
  outliers final: 5
  residues processed: 72
  average time/residue: 0.8550
  time to fit residues: 64.8266
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  523 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 14 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.172895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.140257 restraints weight = 5269.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 2.32
r_work: 0.3733 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4441  Z= 0.125
  Angle     :  0.653  15.388   6079  Z= 0.307
  Chirality :  0.044   0.190    684
  Planarity :  0.004   0.040    717
  Dihedral  :  9.719 105.913    842
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.88 %
    Favored  : 78.65 %
  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:  1.39 (0.38), residues: 519
  helix:  1.85 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -1.37 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.016   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.009   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00167 (    3)
  link_NAG-ASN         : angle       1.42401 (    9)
  hydrogen bonds       : bond        0.03841 (  267)
  hydrogen bonds       : angle       4.17794 (  777)
  SS BOND              : bond        0.00317 (    1)
  SS BOND              : angle       1.13903 (    2)
  covalent geometry    : bond        0.00285 ( 4437)
  covalent geometry    : angle       0.65054 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.5883 (p90)
REVERT: A  133 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7846 (mm)
  outliers start: 11
  outliers final: 6
  residues processed: 65
  average time/residue: 0.8293
  time to fit residues: 56.8388
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  523 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.172828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.139987 restraints weight = 5428.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.36
r_work: 0.3729 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4441  Z= 0.125
  Angle     :  0.658  15.319   6079  Z= 0.309
  Chirality :  0.044   0.190    684
  Planarity :  0.004   0.040    717
  Dihedral  :  9.697 105.594    842
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.78 %
    Favored  : 77.98 %
  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:  1.40 (0.38), residues: 519
  helix:  1.86 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -1.38 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 161 
 PHE   0.025   0.001   PHE A 434 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.009   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    3)
  link_NAG-ASN         : angle       1.45001 (    9)
  hydrogen bonds       : bond        0.03855 (  267)
  hydrogen bonds       : angle       4.19320 (  777)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.63046 (    2)
  covalent geometry    : bond        0.00287 ( 4437)
  covalent geometry    : angle       0.65597 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.5866 (p90)
REVERT: A   72 TYR cc_start: 0.8133 (t80) cc_final: 0.7888 (t80)
REVERT: A  133 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7847 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 66
  average time/residue: 0.8632
  time to fit residues: 60.1388
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  523 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 22 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.174742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.142173 restraints weight = 5283.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.33
r_work: 0.3755 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4441  Z= 0.117
  Angle     :  0.644  15.236   6079  Z= 0.303
  Chirality :  0.043   0.197    684
  Planarity :  0.004   0.039    717
  Dihedral  :  9.551 104.248    842
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 20.45 %
    Favored  : 78.43 %
  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 (0.38), residues: 519
  helix:  1.96 (0.28), residues: 363
  sheet:  None (None), residues: 0
  loop : -1.45 (0.49), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.013   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.009   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    3)
  link_NAG-ASN         : angle       1.45650 (    9)
  hydrogen bonds       : bond        0.03642 (  267)
  hydrogen bonds       : angle       4.16722 (  777)
  SS BOND              : bond        0.00341 (    1)
  SS BOND              : angle       0.67333 (    2)
  covalent geometry    : bond        0.00263 ( 4437)
  covalent geometry    : angle       0.64159 ( 6068)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.6702 (p90)
REVERT: A  133 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (mm)
  outliers start: 5
  outliers final: 3
  residues processed: 59
  average time/residue: 0.9060
  time to fit residues: 56.3095
Evaluate side-chains
  60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  432 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    0.1980
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 540 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.175674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.142979 restraints weight = 5347.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.35
r_work: 0.3768 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4441  Z= 0.112
  Angle     :  0.637  14.867   6079  Z= 0.299
  Chirality :  0.042   0.190    684
  Planarity :  0.004   0.039    717
  Dihedral  :  9.416 102.912    842
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 21.35 %
    Favored  : 77.53 %
  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:  1.52 (0.38), residues: 519
  helix:  1.97 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -1.42 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.027   0.001   PHE A 434 
 TYR   0.013   0.001   TYR A  69 
 ARG   0.009   0.001   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    3)
  link_NAG-ASN         : angle       1.44405 (    9)
  hydrogen bonds       : bond        0.03535 (  267)
  hydrogen bonds       : angle       4.13589 (  777)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.66908 (    2)
  covalent geometry    : bond        0.00246 ( 4437)
  covalent geometry    : angle       0.63526 ( 6068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2619.03 seconds
wall clock time: 46 minutes 10.35 seconds (2770.35 seconds total)