Starting phenix.real_space_refine
on Wed Sep 17 04:19:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1m_44084/09_2025/9b1m_44084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1m_44084/09_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_44084/09_2025/9b1m_44084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1m_44084/09_2025/9b1m_44084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1m_44084/09_2025/9b1m_44084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1m_44084/09_2025/9b1m_44084.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.83, per 1000 atoms: 0.46
  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: 0.36
  Conformation dependent library (CDL) restraints added in 313.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 3.849A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 37
      removed outlier: 3.625A  pdb=" N   SER A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.821A  pdb=" N   ALA A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.664A  pdb=" N   ASP A  97 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.793A  pdb=" N   TRP A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.691A  pdb=" N   GLY A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 3.591A  pdb=" N   PHE A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 220
      removed outlier: 3.540A  pdb=" N   ALA A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 222
      No H-bonds generated for 'chain 'A' and resid 221 through 222'
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 252
      removed outlier: 4.152A  pdb=" N  APHE A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 264 through 273
      removed outlier: 4.101A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 303
      removed outlier: 3.528A  pdb=" N   GLN A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 4.057A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 311 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
    Processing helix  chain 'A' and resid 320 through 325
    Processing helix  chain 'A' and resid 326 through 329
      removed outlier: 3.789A  pdb=" N   GLU A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 329'
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 4.058A  pdb=" N   PHE A 337 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.659A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 371'
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 3.761A  pdb=" N   GLY A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
    Processing helix  chain 'A' and resid 400 through 419
      removed outlier: 3.632A  pdb=" N   THR A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 453
      removed outlier: 3.672A  pdb=" N   ILE A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.652A  pdb=" N   ILE A 477 " --> pdb=" O   ARG A 473 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 483 through 489
      removed outlier: 3.632A  pdb=" N   VAL A 487 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 4.151A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      Proline residue:  A 501  - end of helix
      removed outlier: 3.629A  pdb=" N   LEU A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88

    260 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.48 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:             4.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.680
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.080
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (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
 ARG   0.003   0.001   ARG A 483 
 TYR   0.033   0.002   TYR A 272 
 PHE   0.022   0.002   PHE A 344 
 TRP   0.012   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 424 

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

*********************** 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  : 0.142 
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: 0.5762
  time to fit residues: 42.3274
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  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.160710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108312 restraints weight = 13316.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 4.41
r_work: 0.3067 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2049

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= 0.143
  Angle     :  0.617   8.447   5552  Z= 0.306
  Chirality :  0.040   0.138    653
  Planarity :  0.005   0.042    692
  Dihedral  :  4.636  49.200    574
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.09 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.36), residues: 517
  helix:  0.90 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop :  1.78 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 297 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.014   0.002   PHE A 356 
 TRP   0.014   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4063)
  covalent geometry    : angle       0.61456 ( 5545)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       1.85999 (    4)
  hydrogen bonds       : bond        0.05315 (  260)
  hydrogen bonds       : angle       4.30895 (  753)
  link_NAG-ASN         : bond        0.00550 (    1)
  link_NAG-ASN         : angle       0.95482 (    3)

*********************** 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
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: A  281 ARG cc_start: 0.7692 (mtp-110) cc_final: 0.7272 (mtm-85)
REVERT: A  459 VAL cc_start: 0.8315 (m) cc_final: 0.8062 (p)
REVERT: A  462 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4112 (mpt)
REVERT: A  497 TYR cc_start: 0.8756 (m-80) cc_final: 0.8542 (m-80)
  outliers start: 7
  outliers final: 1
  residues processed: 46
  average time/residue: 0.5173
  time to fit residues: 24.7667
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  : 0.152 
-------------------------------------------------------------------------------
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 16 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 32 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   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 488 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.160491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108386 restraints weight = 12279.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 4.27
r_work: 0.3074 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
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 = 0.41   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 = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2407

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= 0.136
  Angle     :  0.587   8.280   5552  Z= 0.284
  Chirality :  0.039   0.135    653
  Planarity :  0.005   0.038    692
  Dihedral  :  4.108  38.519    574
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.37), residues: 517
  helix:  1.18 (0.27), residues: 371
  sheet: -1.37 (1.46), residues: 10
  loop :  1.74 (0.56), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 343 
 TYR   0.018   0.002   TYR A 272 
 PHE   0.013   0.002   PHE A 358 
 TRP   0.012   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4063)
  covalent geometry    : angle       0.58522 ( 5545)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       1.70813 (    4)
  hydrogen bonds       : bond        0.05038 (  260)
  hydrogen bonds       : angle       4.09439 (  753)
  link_NAG-ASN         : bond        0.00237 (    1)
  link_NAG-ASN         : angle       1.00934 (    3)

*********************** 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: 9
    poor density    : 50
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8780 (t) cc_final: 0.8225 (m)
REVERT: A  219 MET cc_start: 0.6076 (mmp) cc_final: 0.5028 (mtt)
REVERT: A  281 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7417 (mtm-85)
REVERT: A  462 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4216 (mpt)
  outliers start: 9
  outliers final: 3
  residues processed: 54
  average time/residue: 0.3902
  time to fit residues: 22.1868
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
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 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 22 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  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 = 0.3848 r_free = 0.3848 target = 0.161162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.109368 restraints weight = 11567.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.17
r_work: 0.3082 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2684

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     :  0.564   7.829   5552  Z= 0.271
  Chirality :  0.039   0.141    653
  Planarity :  0.005   0.037    692
  Dihedral  :  3.882  33.255    574
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.29 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.37), residues: 517
  helix:  1.57 (0.27), residues: 358
  sheet: -1.74 (1.49), residues: 10
  loop :  1.36 (0.54), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 225 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.012   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4063)
  covalent geometry    : angle       0.56238 ( 5545)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       1.60633 (    4)
  hydrogen bonds       : bond        0.04728 (  260)
  hydrogen bonds       : angle       3.99172 (  753)
  link_NAG-ASN         : bond        0.00230 (    1)
  link_NAG-ASN         : angle       1.07991 (    3)

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

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8786 (t) cc_final: 0.8209 (m)
REVERT: A  219 MET cc_start: 0.6171 (mmp) cc_final: 0.5107 (mtt)
REVERT: A  281 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7471 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7132 (mtt-85)
REVERT: A  462 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4311 (mpt)
  outliers start: 10
  outliers final: 3
  residues processed: 51
  average time/residue: 0.4939
  time to fit residues: 26.2503
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6360

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.161677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111251 restraints weight = 11353.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 4.84
r_work: 0.3071 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    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 = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4066  Z= 0.129
  Angle     :  0.571   8.083   5552  Z= 0.274
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.035    692
  Dihedral  :  3.812  31.667    574
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.29 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.37), residues: 517
  helix:  1.68 (0.27), residues: 358
  sheet: -1.83 (1.58), residues: 10
  loop :  1.41 (0.54), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 343 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.012   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4063)
  covalent geometry    : angle       0.56872 ( 5545)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       1.58658 (    4)
  hydrogen bonds       : bond        0.04726 (  260)
  hydrogen bonds       : angle       3.96817 (  753)
  link_NAG-ASN         : bond        0.00222 (    1)
  link_NAG-ASN         : angle       1.10723 (    3)

*********************** 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  : 0.152 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8739 (t) cc_final: 0.8160 (m)
REVERT: A  281 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7406 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7095 (mtt-85)
REVERT: A  462 MET cc_start: 0.4989 (OUTLIER) cc_final: 0.4280 (mpt)
  outliers start: 9
  outliers final: 3
  residues processed: 48
  average time/residue: 0.4926
  time to fit residues: 24.5829
Evaluate side-chains
  48 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  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 26 optimal weight:    0.0070
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.161744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.109145 restraints weight = 13486.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 4.47
r_work: 0.3083 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4066  Z= 0.125
  Angle     :  0.553   7.091   5552  Z= 0.265
  Chirality :  0.038   0.139    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.694  29.087    574
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.48 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.37), residues: 517
  helix:  1.73 (0.27), residues: 359
  sheet: -1.95 (1.61), residues: 10
  loop :  1.48 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 225 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.013   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4063)
  covalent geometry    : angle       0.55088 ( 5545)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       1.54837 (    4)
  hydrogen bonds       : bond        0.04557 (  260)
  hydrogen bonds       : angle       3.92730 (  753)
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       1.02794 (    3)

*********************** 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
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8742 (t) cc_final: 0.8139 (m)
REVERT: A  281 ARG cc_start: 0.7742 (mtp-110) cc_final: 0.7438 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7191 (mtt-85)
REVERT: A  462 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4410 (mpt)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.4422
  time to fit residues: 22.1977
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   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 488 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.160892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.109332 restraints weight = 11016.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 4.07
r_work: 0.3084 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2896

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     :  0.547   6.590   5552  Z= 0.266
  Chirality :  0.039   0.139    653
  Planarity :  0.004   0.034    692
  Dihedral  :  3.691  28.343    574
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.37), residues: 517
  helix:  1.75 (0.27), residues: 358
  sheet: -1.98 (1.67), residues: 10
  loop :  1.50 (0.55), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 225 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.013   0.001   PHE A 358 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4063)
  covalent geometry    : angle       0.54432 ( 5545)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       1.89825 (    4)
  hydrogen bonds       : bond        0.04657 (  260)
  hydrogen bonds       : angle       3.95292 (  753)
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       1.08609 (    3)

*********************** 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
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  120 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7871 (t0)
REVERT: A  126 SER cc_start: 0.8776 (t) cc_final: 0.8172 (m)
REVERT: A  281 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7465 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7283 (mtt-85)
REVERT: A  462 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4453 (mpt)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.4796
  time to fit residues: 22.9604
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
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  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 7 optimal weight:    0.0010
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.165283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.112463 restraints weight = 10933.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 4.27
r_work: 0.3102 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
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 = 0.41   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 = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4066  Z= 0.115
  Angle     :  0.535   8.823   5552  Z= 0.256
  Chirality :  0.038   0.141    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.591  26.660    574
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.37), residues: 517
  helix:  1.91 (0.27), residues: 359
  sheet: -1.59 (1.79), residues: 10
  loop :  1.49 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 225 
 TYR   0.022   0.002   TYR A 272 
 PHE   0.012   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4063)
  covalent geometry    : angle       0.53399 ( 5545)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       1.40029 (    4)
  hydrogen bonds       : bond        0.04325 (  260)
  hydrogen bonds       : angle       3.89380 (  753)
  link_NAG-ASN         : bond        0.00239 (    1)
  link_NAG-ASN         : angle       1.01389 (    3)

*********************** 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
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.8161 (mm110) cc_final: 0.7911 (mp10)
REVERT: A  120 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7840 (t0)
REVERT: A  126 SER cc_start: 0.8680 (t) cc_final: 0.8066 (m)
REVERT: A  281 ARG cc_start: 0.7687 (mtp-110) cc_final: 0.7358 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7245 (mtt-85)
REVERT: A  462 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4410 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.4726
  time to fit residues: 23.6693
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.160011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.111383 restraints weight = 6056.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.11
r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4066  Z= 0.153
  Angle     :  0.571   8.195   5552  Z= 0.275
  Chirality :  0.039   0.138    653
  Planarity :  0.004   0.035    692
  Dihedral  :  3.626  26.418    574
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.24 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.37), residues: 517
  helix:  1.78 (0.27), residues: 356
  sheet: -1.53 (1.84), residues: 10
  loop :  1.38 (0.55), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 225 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.014   0.002   PHE A 358 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.005   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4063)
  covalent geometry    : angle       0.56904 ( 5545)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       1.55676 (    4)
  hydrogen bonds       : bond        0.04832 (  260)
  hydrogen bonds       : angle       3.95361 (  753)
  link_NAG-ASN         : bond        0.00168 (    1)
  link_NAG-ASN         : angle       1.13472 (    3)

*********************** 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
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8100 (tp30)
REVERT: A   90 GLN cc_start: 0.8294 (mm110) cc_final: 0.8049 (mp10)
REVERT: A  120 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (t0)
REVERT: A  126 SER cc_start: 0.8814 (t) cc_final: 0.8207 (m)
REVERT: A  281 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7508 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7328 (mtt-85)
REVERT: A  462 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4642 (mpt)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 0.6049
  time to fit residues: 30.5418
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  : 0.088 
-------------------------------------------------------------------------------
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  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0770
   chunk 32 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.161581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.111257 restraints weight = 8246.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 3.62
r_work: 0.3121 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3120

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= 0.128
  Angle     :  0.574   8.307   5552  Z= 0.275
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.607  26.051    574
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.37), residues: 517
  helix:  1.82 (0.27), residues: 359
  sheet: -1.54 (1.74), residues: 10
  loop :  1.47 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 225 
 TYR   0.022   0.002   TYR A 272 
 PHE   0.012   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4063)
  covalent geometry    : angle       0.57254 ( 5545)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       1.45227 (    4)
  hydrogen bonds       : bond        0.04556 (  260)
  hydrogen bonds       : angle       3.94380 (  753)
  link_NAG-ASN         : bond        0.00232 (    1)
  link_NAG-ASN         : angle       1.02682 (    3)

********************** 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: 10
    poor density    : 43
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8125 (tp30)
REVERT: A   90 GLN cc_start: 0.8325 (mm110) cc_final: 0.8084 (mp10)
REVERT: A  120 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7909 (t0)
REVERT: A  126 SER cc_start: 0.8788 (t) cc_final: 0.8180 (m)
REVERT: A  281 ARG cc_start: 0.7839 (mtp-110) cc_final: 0.7508 (mtm-85)
REVERT: A  297 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7361 (mtt-85)
REVERT: A  462 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4546 (mpt)
  outliers start: 10
  outliers final: 4
  residues processed: 47
  average time/residue: 0.5761
  time to fit residues: 28.0746
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  297 ARG
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 28 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.161960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.112780 restraints weight = 6544.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.25
r_work: 0.3154 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4066  Z= 0.128
  Angle     :  0.574   8.233   5552  Z= 0.275
  Chirality :  0.038   0.140    653
  Planarity :  0.004   0.033    692
  Dihedral  :  3.558  24.773    574
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.37), residues: 517
  helix:  1.87 (0.27), residues: 359
  sheet: -1.60 (1.69), residues: 10
  loop :  1.53 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 225 
 TYR   0.022   0.002   TYR A 272 
 PHE   0.013   0.001   PHE A 358 
 TRP   0.011   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4063)
  covalent geometry    : angle       0.57303 ( 5545)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       1.44901 (    4)
  hydrogen bonds       : bond        0.04507 (  260)
  hydrogen bonds       : angle       3.90824 (  753)
  link_NAG-ASN         : bond        0.00219 (    1)
  link_NAG-ASN         : angle       1.03279 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1578.01 seconds
wall clock time: 27 minutes 40.44 seconds (1660.44 seconds total)