Starting phenix.real_space_refine
on Tue Feb  3 15:35:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nbo_49234/02_2026/9nbo_49234_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nbo_49234/02_2026/9nbo_49234.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/9nbo_49234/02_2026/9nbo_49234.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nbo_49234/02_2026/9nbo_49234.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nbo_49234/02_2026/9nbo_49234_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nbo_49234/02_2026/9nbo_49234_neut.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=   0.015
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: 7
    Type Number    sf(0)   Gaussians
     As      1      7.32       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      13      5.16       5
     C    2735      2.51       5
     N     781      2.21       5
     O     842      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4380
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4310
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 34, 'TRANS': 536}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 70
          Unusual residues: {' MG': 2, 'ARS': 1, 'ATP': 2}
          Classifications: {'undetermined': 5, 'water': 5}
          Link IDs: {None: 9}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    825  SG  CYS A 114      28.789  33.296  25.304  1.00 78.14           S
  ATOM   1268  SG  CYS A 173      30.791  35.012  22.268  1.00 88.85           S
  ATOM   3086  SG  CYS A 422      31.827  35.718  24.826  1.00 81.75           S

  Time building chain proxies: 1.09, per 1000 atoms: 0.25
  Number of scatterers: 4380
  At special positions: 0
  Unit cell: (59.8, 76.05, 89.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     As      1     32.98
     S      13     16.00
     P       6     15.00
     Mg      2     11.99
     O     842      8.00
     N     781      7.00
     C    2735      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 266.0 milliseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1062

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      55.2% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 36
    Processing helix  chain 'A' and resid 50 through 56
      removed outlier: 3.924A  pdb=" N   VAL A  54 " --> pdb=" O   ASN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 93 through 95
      No H-bonds generated for 'chain 'A' and resid 93 through 95'
    Processing helix  chain 'A' and resid 99 through 110
    Processing helix  chain 'A' and resid 112 through 130
      removed outlier: 3.687A  pdb=" N   THR A 116 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 120 " --> pdb=" O   THR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 4.200A  pdb=" N   ARG A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 179 through 182
    Processing helix  chain 'A' and resid 183 through 195
    Processing helix  chain 'A' and resid 209 through 227
    Processing helix  chain 'A' and resid 240 through 244
    Processing helix  chain 'A' and resid 247 through 263
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 314 through 326
      removed outlier: 4.203A  pdb=" N   LEU A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP A 325 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 354
    Processing helix  chain 'A' and resid 368 through 372
    Processing helix  chain 'A' and resid 386 through 403
    Processing helix  chain 'A' and resid 407 through 419
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 4.431A  pdb=" N   GLU A 425 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.715A  pdb=" N   ASP A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 472
    Processing helix  chain 'A' and resid 481 through 487
      removed outlier: 3.686A  pdb=" N   GLN A 485 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 518
    Processing helix  chain 'A' and resid 538 through 558
      removed outlier: 4.345A  pdb=" N   ARG A 550 " --> pdb=" O   ALA A 546 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLU A 551 " --> pdb=" O   ASN A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 582
      removed outlier: 4.363A  pdb=" N   ARG A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
      removed outlier: 6.444A  pdb=" N   VAL A  40 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   LEU A  75 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU A  42 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU A  41 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ASP A 143 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL A  43 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   MET A  12 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   PHE A  11 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   VAL A 203 " --> pdb=" O   PHE A  11 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   PHE A  13 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL A 205 " --> pdb=" O   PHE A  13 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   THR A  15 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 8.889A  pdb=" N   ARG A 207 " --> pdb=" O   THR A  15 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A 276 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE A 235 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 382
      removed outlier: 6.842A  pdb=" N   VAL A 358 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   HIS A 359 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   ASP A 447 " --> pdb=" O   HIS A 359 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   THR A 361 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU A 329 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   LEU A 495 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   MET A 331 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   VAL A 497 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   MET A 333 " --> pdb=" O   VAL A 497 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   LEU A 499 " --> pdb=" O   MET A 333 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA A 524 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    645 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: 0.65

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1496
        1.34 -     1.46: 792
        1.46 -     1.58: 2131
        1.58 -     1.69: 9
        1.69 -     1.81: 22
  Bond restraints: 4450
  Sorted by residual:
  bond pdb=" C1' ATP A 602 "
       pdb=" O4' ATP A 602 "
    ideal  model  delta    sigma   weight residual
    1.416  1.398  0.018 1.30e-02 5.92e+03 1.82e+00
  bond pdb=" C1' ATP A 601 "
       pdb=" O4' ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.416  1.398  0.018 1.30e-02 5.92e+03 1.82e+00
  bond pdb=" CG  LEU A 332 "
       pdb=" CD1 LEU A 332 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.55e-01
  bond pdb=" C   THR A 503 "
       pdb=" O   THR A 503 "
    ideal  model  delta    sigma   weight residual
    1.244  1.236  0.008 9.80e-03 1.04e+04 6.43e-01
  bond pdb=" C4' ATP A 601 "
       pdb=" O4' ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.444  1.435  0.009 1.10e-02 8.26e+03 6.38e-01
  ... (remaining 4445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 5946
        1.35 -     2.70: 79
        2.70 -     4.05: 35
        4.05 -     5.40: 6
        5.40 -     6.75: 7
  Bond angle restraints: 6073
  Sorted by residual:
  angle pdb=" C3' ATP A 601 "
        pdb=" C4' ATP A 601 "
        pdb=" C5' ATP A 601 "
      ideal   model   delta    sigma   weight residual
     115.19  110.09    5.10 1.76e+00 3.23e-01 8.41e+00
  angle pdb=" C3' ATP A 602 "
        pdb=" C4' ATP A 602 "
        pdb=" C5' ATP A 602 "
      ideal   model   delta    sigma   weight residual
     115.19  110.15    5.04 1.76e+00 3.23e-01 8.20e+00
  angle pdb=" C5' ATP A 601 "
        pdb=" C4' ATP A 601 "
        pdb=" O4' ATP A 601 "
      ideal   model   delta    sigma   weight residual
     109.53  105.52    4.01 1.44e+00 4.84e-01 7.80e+00
  angle pdb=" C3' ATP A 601 "
        pdb=" C2' ATP A 601 "
        pdb=" O2' ATP A 601 "
      ideal   model   delta    sigma   weight residual
     111.83  105.08    6.75 2.67e+00 1.40e-01 6.40e+00
  angle pdb=" C3' ATP A 602 "
        pdb=" C2' ATP A 602 "
        pdb=" O2' ATP A 602 "
      ideal   model   delta    sigma   weight residual
     111.83  105.20    6.63 2.67e+00 1.40e-01 6.17e+00
  ... (remaining 6068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 2500
       17.56 -    35.12: 196
       35.12 -    52.68: 32
       52.68 -    70.24: 16
       70.24 -    87.80: 6
  Dihedral angle restraints: 2750
    sinusoidal: 1114
      harmonic: 1636
  Sorted by residual:
  dihedral pdb=" CA  ASP A 274 "
           pdb=" CB  ASP A 274 "
           pdb=" CG  ASP A 274 "
           pdb=" OD1 ASP A 274 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.85   59.85     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" N   GLN A 471 "
           pdb=" CA  GLN A 471 "
           pdb=" CB  GLN A 471 "
           pdb=" CG  GLN A 471 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.65   50.65     3      1.50e+01 4.44e-03 8.92e+00
  dihedral pdb=" CA  ASP A 317 "
           pdb=" CB  ASP A 317 "
           pdb=" CG  ASP A 317 "
           pdb=" OD1 ASP A 317 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -77.31   47.31     1      2.00e+01 2.50e-03 7.73e+00
  ... (remaining 2747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 620
       0.055 -    0.111: 78
       0.111 -    0.166: 22
       0.166 -    0.221: 0
       0.221 -    0.277: 6
  Chirality restraints: 726
  Sorted by residual:
  chirality pdb=" C2' ATP A 601 "
            pdb=" C1' ATP A 601 "
            pdb=" C3' ATP A 601 "
            pdb=" O2' ATP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C2' ATP A 602 "
            pdb=" C1' ATP A 602 "
            pdb=" C3' ATP A 602 "
            pdb=" O2' ATP A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.95    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C3' ATP A 602 "
            pdb=" C2' ATP A 602 "
            pdb=" C4' ATP A 602 "
            pdb=" O3' ATP A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.90    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 723 not shown)

  Planarity restraints: 783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 432 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   PHE A 432 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE A 432 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER A 433 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 431 "   -0.006 2.00e-02 2.50e+03   1.20e-02 1.45e+00
        pdb=" C   ALA A 431 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ALA A 431 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PHE A 432 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 503 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO A 504 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 504 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 504 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 780 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 26
        2.49 -     3.09: 3240
        3.09 -     3.69: 6619
        3.69 -     4.30: 9911
        4.30 -     4.90: 16788
  Nonbonded interactions: 36584
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  23 "
            pdb="MG    MG A 604 "
     model   vdw
     1.886 2.170
  nonbonded pdb=" OG1 THR A 341 "
            pdb="MG    MG A 603 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" O2B ATP A 602 "
            pdb="MG    MG A 603 "
     model   vdw
     2.013 2.170
  nonbonded pdb=" OG  SER A  44 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" NH2 ARG A 152 "
            pdb=" O   PRO A 421 "
     model   vdw
     2.169 3.120
  ... (remaining 36579 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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.110
  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:6.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
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      :  0.003   0.031   4450  Z= 0.142
  Angle     :  0.544   6.752   6073  Z= 0.270
  Chirality :  0.048   0.277    726
  Planarity :  0.004   0.029    783
  Dihedral  : 14.111  87.804   1688
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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 are not related in a simple way.
  whole:  1.06 (0.38), residues: 565
  helix:  1.69 (0.33), residues: 272
  sheet: -1.29 (0.54), residues: 80
  loop :  0.41 (0.48), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 411 
 TYR   0.005   0.001   TYR A  86 
 PHE   0.008   0.001   PHE A   4 
 TRP   0.004   0.001   TRP A 525 
 HIS   0.003   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4450)
  covalent geometry    : angle       0.54394 ( 6073)
  hydrogen bonds       : bond        0.11400 (  222)
  hydrogen bonds       : angle       6.03912 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7781 (tt0) cc_final: 0.7555 (pt0)
REVERT: A   39 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7310 (mtm-85)
REVERT: A   80 GLU cc_start: 0.7136 (tp30) cc_final: 0.6096 (pm20)
REVERT: A  188 LYS cc_start: 0.7417 (ttpt) cc_final: 0.6815 (tptt)
REVERT: A  255 GLU cc_start: 0.7814 (tt0) cc_final: 0.7304 (tp30)
REVERT: A  388 HIS cc_start: 0.7325 (m-70) cc_final: 0.6787 (m-70)
REVERT: A  393 ARG cc_start: 0.7580 (mtp180) cc_final: 0.6737 (ttt-90)
REVERT: A  399 LEU cc_start: 0.7800 (mt) cc_final: 0.7580 (mp)
REVERT: A  503 THR cc_start: 0.8536 (m) cc_final: 0.8259 (p)
REVERT: A  558 HIS cc_start: 0.7467 (t-90) cc_final: 0.6839 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.4777
  time to fit residues: 38.0013
Evaluate side-chains
  58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 327 HIS
A 368 HIS
A 397 HIS
A 553 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.133281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.101754 restraints weight = 4454.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.70
r_work: 0.2885 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4450  Z= 0.146
  Angle     :  0.514   7.892   6073  Z= 0.261
  Chirality :  0.043   0.145    726
  Planarity :  0.005   0.036    783
  Dihedral  : 10.354  87.969    676
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  7.51 %
    Favored  : 89.85 %
  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 are not related in a simple way.
  whole:  0.92 (0.36), residues: 565
  helix:  1.74 (0.31), residues: 292
  sheet: -1.28 (0.54), residues: 79
  loop : -0.19 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  10 
 TYR   0.004   0.001   TYR A 187 
 PHE   0.011   0.001   PHE A   4 
 TRP   0.004   0.001   TRP A 525 
 HIS   0.002   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4450)
  covalent geometry    : angle       0.51376 ( 6073)
  hydrogen bonds       : bond        0.03550 (  222)
  hydrogen bonds       : angle       4.37837 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7888 (tt0) cc_final: 0.7501 (pt0)
REVERT: A   39 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7329 (mtm-85)
REVERT: A   80 GLU cc_start: 0.7162 (tp30) cc_final: 0.6023 (pm20)
REVERT: A   87 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6324 (mtp180)
REVERT: A  184 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7141 (ttt90)
REVERT: A  255 GLU cc_start: 0.7809 (tt0) cc_final: 0.7209 (tp30)
REVERT: A  388 HIS cc_start: 0.7300 (m-70) cc_final: 0.6773 (m-70)
REVERT: A  393 ARG cc_start: 0.7561 (mtp180) cc_final: 0.6811 (ttt-90)
REVERT: A  503 THR cc_start: 0.8584 (m) cc_final: 0.8304 (p)
REVERT: A  558 HIS cc_start: 0.7472 (t-90) cc_final: 0.6715 (m-70)
  outliers start: 12
  outliers final: 3
  residues processed: 66
  average time/residue: 0.5721
  time to fit residues: 39.0359
Evaluate side-chains
  60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 26 optimal weight:    0.0060
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0030
   chunk 55 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0470
   chunk 46 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.3706

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.135613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.104509 restraints weight = 4420.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.70
r_work: 0.2924 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4450  Z= 0.104
  Angle     :  0.469   7.112   6073  Z= 0.238
  Chirality :  0.041   0.136    726
  Planarity :  0.004   0.040    783
  Dihedral  :  9.846  80.538    676
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  :  8.83 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.37), residues: 565
  helix:  1.78 (0.30), residues: 299
  sheet: -1.13 (0.54), residues: 79
  loop : -0.24 (0.49), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 437 
 TYR   0.006   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.005   0.001   TRP A 525 
 HIS   0.012   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4450)
  covalent geometry    : angle       0.46939 ( 6073)
  hydrogen bonds       : bond        0.02968 (  222)
  hydrogen bonds       : angle       4.00382 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7816 (tt0) cc_final: 0.7467 (pt0)
REVERT: A   39 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7361 (mtm-85)
REVERT: A   80 GLU cc_start: 0.7167 (tp30) cc_final: 0.6030 (pm20)
REVERT: A  188 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6804 (tptt)
REVERT: A  215 GLU cc_start: 0.7485 (tt0) cc_final: 0.6735 (mm-30)
REVERT: A  255 GLU cc_start: 0.7807 (tt0) cc_final: 0.7191 (tp30)
REVERT: A  388 HIS cc_start: 0.7260 (m-70) cc_final: 0.6731 (m-70)
REVERT: A  392 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6191 (mm-30)
REVERT: A  393 ARG cc_start: 0.7624 (mtp180) cc_final: 0.6895 (ttt-90)
REVERT: A  503 THR cc_start: 0.8603 (m) cc_final: 0.8288 (p)
REVERT: A  537 LYS cc_start: 0.7673 (mttt) cc_final: 0.7309 (mmtp)
REVERT: A  549 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7609 (mp)
REVERT: A  558 HIS cc_start: 0.7460 (t-90) cc_final: 0.6667 (m-70)
  outliers start: 14
  outliers final: 2
  residues processed: 70
  average time/residue: 0.6608
  time to fit residues: 47.7107
Evaluate side-chains
  61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0980
   chunk 46 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 327 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.134806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.103828 restraints weight = 4322.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.68
r_work: 0.2930 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4450  Z= 0.117
  Angle     :  0.469   6.460   6073  Z= 0.236
  Chirality :  0.041   0.136    726
  Planarity :  0.004   0.044    783
  Dihedral  :  9.861  80.856    676
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  :  9.93 %
    Favored  : 87.20 %
  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 are not related in a simple way.
  whole:  1.12 (0.36), residues: 565
  helix:  1.89 (0.30), residues: 293
  sheet: -1.12 (0.54), residues: 79
  loop : -0.09 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  10 
 TYR   0.007   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.003   0.001   TRP A 525 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4450)
  covalent geometry    : angle       0.46868 ( 6073)
  hydrogen bonds       : bond        0.03016 (  222)
  hydrogen bonds       : angle       3.95790 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7777 (tt0) cc_final: 0.7472 (pt0)
REVERT: A   39 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7351 (mtm-85)
REVERT: A   80 GLU cc_start: 0.7193 (tp30) cc_final: 0.6059 (pm20)
REVERT: A  181 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7390 (tm-30)
REVERT: A  188 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6816 (tptt)
REVERT: A  215 GLU cc_start: 0.7512 (tt0) cc_final: 0.6767 (mm-30)
REVERT: A  255 GLU cc_start: 0.7808 (tt0) cc_final: 0.7196 (tp30)
REVERT: A  388 HIS cc_start: 0.7275 (m-70) cc_final: 0.6768 (m-70)
REVERT: A  393 ARG cc_start: 0.7623 (mtp180) cc_final: 0.6871 (ttt-90)
REVERT: A  503 THR cc_start: 0.8601 (m) cc_final: 0.8275 (p)
REVERT: A  549 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7630 (mp)
REVERT: A  558 HIS cc_start: 0.7462 (t-90) cc_final: 0.6697 (m170)
  outliers start: 13
  outliers final: 3
  residues processed: 69
  average time/residue: 0.5884
  time to fit residues: 42.0447
Evaluate side-chains
  58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.134523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.101754 restraints weight = 4197.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.77
r_work: 0.3046 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4450  Z= 0.193
  Angle     :  0.521   8.276   6073  Z= 0.262
  Chirality :  0.044   0.151    726
  Planarity :  0.005   0.047    783
  Dihedral  : 10.599  89.684    676
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  :  9.93 %
    Favored  : 86.31 %
  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 are not related in a simple way.
  whole:  0.77 (0.36), residues: 565
  helix:  1.65 (0.30), residues: 293
  sheet: -1.25 (0.53), residues: 79
  loop : -0.37 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 256 
 TYR   0.006   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.002   0.001   TRP A 160 
 HIS   0.009   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4450)
  covalent geometry    : angle       0.52134 ( 6073)
  hydrogen bonds       : bond        0.03522 (  222)
  hydrogen bonds       : angle       4.15060 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7946 (tt0) cc_final: 0.7677 (pt0)
REVERT: A   39 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7598 (mtm-85)
REVERT: A   64 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8640 (p)
REVERT: A   80 GLU cc_start: 0.7386 (tp30) cc_final: 0.6307 (pm20)
REVERT: A   87 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6598 (mtp180)
REVERT: A  107 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: A  188 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7123 (tptt)
REVERT: A  215 GLU cc_start: 0.7573 (tt0) cc_final: 0.6959 (mm-30)
REVERT: A  255 GLU cc_start: 0.7971 (tt0) cc_final: 0.7473 (tp30)
REVERT: A  388 HIS cc_start: 0.7523 (m-70) cc_final: 0.7046 (m-70)
REVERT: A  393 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7067 (ttt-90)
REVERT: A  503 THR cc_start: 0.8682 (m) cc_final: 0.8362 (p)
REVERT: A  549 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7776 (mp)
REVERT: A  558 HIS cc_start: 0.7516 (t-90) cc_final: 0.6894 (m-70)
REVERT: A  571 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7486 (mp0)
  outliers start: 17
  outliers final: 6
  residues processed: 62
  average time/residue: 0.5789
  time to fit residues: 37.0944
Evaluate side-chains
  63 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  400 GLU
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.134502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.101662 restraints weight = 4256.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.79
r_work: 0.3108 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4450  Z= 0.169
  Angle     :  0.503   7.653   6073  Z= 0.254
  Chirality :  0.043   0.146    726
  Planarity :  0.005   0.047    783
  Dihedral  : 10.687  89.450    676
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  :  9.49 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.36), residues: 565
  helix:  1.63 (0.30), residues: 293
  sheet: -1.40 (0.53), residues: 79
  loop : -0.32 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 256 
 TYR   0.007   0.001   TYR A  86 
 PHE   0.010   0.001   PHE A   4 
 TRP   0.002   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4450)
  covalent geometry    : angle       0.50299 ( 6073)
  hydrogen bonds       : bond        0.03368 (  222)
  hydrogen bonds       : angle       4.11340 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7994 (tt0) cc_final: 0.7690 (pt0)
REVERT: A   39 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7649 (mtm-85)
REVERT: A   64 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8630 (p)
REVERT: A   80 GLU cc_start: 0.7469 (tp30) cc_final: 0.6388 (pm20)
REVERT: A   87 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6661 (mtp180)
REVERT: A  107 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7508 (mt-10)
REVERT: A  188 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7170 (tptt)
REVERT: A  215 GLU cc_start: 0.7606 (tt0) cc_final: 0.7062 (mm-30)
REVERT: A  255 GLU cc_start: 0.8024 (tt0) cc_final: 0.7507 (tp30)
REVERT: A  388 HIS cc_start: 0.7580 (m-70) cc_final: 0.7116 (m-70)
REVERT: A  392 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6597 (mm-30)
REVERT: A  393 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7126 (ttt-90)
REVERT: A  503 THR cc_start: 0.8686 (m) cc_final: 0.8374 (p)
REVERT: A  549 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7754 (mp)
REVERT: A  558 HIS cc_start: 0.7544 (t-90) cc_final: 0.6923 (m170)
REVERT: A  571 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7525 (mp0)
  outliers start: 18
  outliers final: 7
  residues processed: 68
  average time/residue: 0.5715
  time to fit residues: 40.2638
Evaluate side-chains
  68 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  400 GLU
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  510 LYS
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0770
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.9944

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.148160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.115746 restraints weight = 4151.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.74
r_work: 0.3151 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4450  Z= 0.150
  Angle     :  0.497   8.677   6073  Z= 0.250
  Chirality :  0.042   0.142    726
  Planarity :  0.005   0.046    783
  Dihedral  : 10.551  88.352    676
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  :  9.93 %
    Favored  : 85.87 %
  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 are not related in a simple way.
  whole:  0.91 (0.36), residues: 565
  helix:  1.77 (0.30), residues: 287
  sheet: -1.44 (0.54), residues: 79
  loop : -0.12 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 256 
 TYR   0.007   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.002   0.001   TRP A 525 
 HIS   0.012   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4450)
  covalent geometry    : angle       0.49688 ( 6073)
  hydrogen bonds       : bond        0.03209 (  222)
  hydrogen bonds       : angle       4.03934 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7971 (tt0) cc_final: 0.7648 (pt0)
REVERT: A   39 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7643 (mtm-85)
REVERT: A   64 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8601 (p)
REVERT: A   80 GLU cc_start: 0.7403 (tp30) cc_final: 0.6279 (pm20)
REVERT: A   87 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6617 (mtp180)
REVERT: A  107 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7436 (mt-10)
REVERT: A  188 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7096 (tptt)
REVERT: A  215 GLU cc_start: 0.7655 (tt0) cc_final: 0.7029 (mm-30)
REVERT: A  255 GLU cc_start: 0.8042 (tt0) cc_final: 0.7507 (tp30)
REVERT: A  388 HIS cc_start: 0.7549 (m-70) cc_final: 0.7088 (m-70)
REVERT: A  392 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6607 (mm-30)
REVERT: A  393 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7110 (ttt-90)
REVERT: A  503 THR cc_start: 0.8706 (m) cc_final: 0.8399 (p)
REVERT: A  549 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7743 (mp)
REVERT: A  558 HIS cc_start: 0.7591 (t-90) cc_final: 0.6917 (m170)
REVERT: A  571 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7402 (mp0)
  outliers start: 19
  outliers final: 6
  residues processed: 66
  average time/residue: 0.6121
  time to fit residues: 41.8484
Evaluate side-chains
  65 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  400 GLU
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  582 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.0570
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 327 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.149737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117179 restraints weight = 4130.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.78
r_work: 0.3173 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4450  Z= 0.119
  Angle     :  0.472   8.039   6073  Z= 0.237
  Chirality :  0.041   0.136    726
  Planarity :  0.005   0.045    783
  Dihedral  : 10.171  83.811    676
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 10.60 %
    Favored  : 85.21 %
  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 are not related in a simple way.
  whole:  1.01 (0.36), residues: 565
  helix:  1.87 (0.31), residues: 287
  sheet: -1.39 (0.54), residues: 79
  loop : -0.10 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 256 
 TYR   0.008   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.003   0.001   TRP A 525 
 HIS   0.002   0.000   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4450)
  covalent geometry    : angle       0.47221 ( 6073)
  hydrogen bonds       : bond        0.02939 (  222)
  hydrogen bonds       : angle       3.93332 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7918 (tt0) cc_final: 0.7639 (pt0)
REVERT: A   39 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7625 (mtm-85)
REVERT: A   64 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8605 (p)
REVERT: A   80 GLU cc_start: 0.7375 (tp30) cc_final: 0.6309 (pm20)
REVERT: A   87 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6628 (mtp180)
REVERT: A  107 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7455 (mt-10)
REVERT: A  181 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7520 (tm-30)
REVERT: A  188 LYS cc_start: 0.7563 (ttpt) cc_final: 0.7148 (tptt)
REVERT: A  198 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: A  215 GLU cc_start: 0.7620 (tt0) cc_final: 0.7060 (mm-30)
REVERT: A  255 GLU cc_start: 0.8014 (tt0) cc_final: 0.7500 (tp30)
REVERT: A  388 HIS cc_start: 0.7549 (m-70) cc_final: 0.7091 (m-70)
REVERT: A  392 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6574 (mm-30)
REVERT: A  393 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7080 (ttt-90)
REVERT: A  503 THR cc_start: 0.8704 (m) cc_final: 0.8386 (p)
REVERT: A  558 HIS cc_start: 0.7549 (t-90) cc_final: 0.6915 (m-70)
  outliers start: 19
  outliers final: 7
  residues processed: 70
  average time/residue: 0.5965
  time to fit residues: 43.2538
Evaluate side-chains
  67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  582 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 46 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 54 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120648 restraints weight = 4088.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.74
r_work: 0.3164 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4450  Z= 0.107
  Angle     :  0.460   7.586   6073  Z= 0.233
  Chirality :  0.040   0.135    726
  Planarity :  0.004   0.045    783
  Dihedral  :  9.777  78.953    676
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.36 %
    Favored  : 84.77 %
  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 are not related in a simple way.
  whole:  1.15 (0.37), residues: 565
  helix:  2.01 (0.31), residues: 287
  sheet: -1.34 (0.54), residues: 79
  loop : -0.06 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.007   0.001   TYR A  86 
 PHE   0.008   0.001   PHE A   4 
 TRP   0.003   0.001   TRP A 525 
 HIS   0.009   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 4450)
  covalent geometry    : angle       0.46012 ( 6073)
  hydrogen bonds       : bond        0.02733 (  222)
  hydrogen bonds       : angle       3.80341 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7858 (tt0) cc_final: 0.7613 (pt0)
REVERT: A   39 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7561 (mtm-85)
REVERT: A   64 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8592 (p)
REVERT: A   80 GLU cc_start: 0.7296 (tp30) cc_final: 0.6541 (tp30)
REVERT: A   87 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7709 (mtm-85)
REVERT: A  107 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7417 (mt-10)
REVERT: A  181 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7483 (tm-30)
REVERT: A  188 LYS cc_start: 0.7543 (ttpt) cc_final: 0.7121 (tptt)
REVERT: A  198 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7873 (mp)
REVERT: A  215 GLU cc_start: 0.7596 (tt0) cc_final: 0.7016 (mm-30)
REVERT: A  255 GLU cc_start: 0.7977 (tt0) cc_final: 0.7448 (tp30)
REVERT: A  388 HIS cc_start: 0.7510 (m-70) cc_final: 0.7036 (m-70)
REVERT: A  392 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6472 (mm-30)
REVERT: A  393 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7020 (ttt-90)
REVERT: A  503 THR cc_start: 0.8677 (m) cc_final: 0.8365 (p)
REVERT: A  537 LYS cc_start: 0.7864 (mttt) cc_final: 0.7566 (mmtp)
REVERT: A  558 HIS cc_start: 0.7529 (t-90) cc_final: 0.6905 (m170)
  outliers start: 13
  outliers final: 5
  residues processed: 67
  average time/residue: 0.5948
  time to fit residues: 41.3405
Evaluate side-chains
  66 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 327 HIS
A 397 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.148811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116884 restraints weight = 4156.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.70
r_work: 0.3167 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4450  Z= 0.216
  Angle     :  0.546  10.307   6073  Z= 0.272
  Chirality :  0.045   0.156    726
  Planarity :  0.005   0.050    783
  Dihedral  : 10.891  86.346    676
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.80 %
    Favored  : 84.33 %
  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 are not related in a simple way.
  whole:  0.83 (0.36), residues: 565
  helix:  1.78 (0.30), residues: 281
  sheet: -1.57 (0.54), residues: 79
  loop : -0.18 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 256 
 TYR   0.006   0.001   TYR A  86 
 PHE   0.010   0.002   PHE A   4 
 TRP   0.002   0.001   TRP A 525 
 HIS   0.003   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 4450)
  covalent geometry    : angle       0.54606 ( 6073)
  hydrogen bonds       : bond        0.03583 (  222)
  hydrogen bonds       : angle       4.12056 (  645)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.7972 (tt0) cc_final: 0.7693 (pt0)
REVERT: A   39 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7633 (mtm-85)
REVERT: A   64 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8614 (p)
REVERT: A   80 GLU cc_start: 0.7412 (tp30) cc_final: 0.6364 (pm20)
REVERT: A   87 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6703 (mtp180)
REVERT: A  107 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: A  188 LYS cc_start: 0.7604 (ttpt) cc_final: 0.7194 (tptt)
REVERT: A  215 GLU cc_start: 0.7598 (tt0) cc_final: 0.7055 (mm-30)
REVERT: A  255 GLU cc_start: 0.8017 (tt0) cc_final: 0.7538 (tp30)
REVERT: A  388 HIS cc_start: 0.7563 (m-70) cc_final: 0.7105 (m-70)
REVERT: A  392 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6613 (mm-30)
REVERT: A  393 ARG cc_start: 0.7802 (mtp180) cc_final: 0.7097 (ttt-90)
REVERT: A  503 THR cc_start: 0.8703 (m) cc_final: 0.8398 (p)
REVERT: A  558 HIS cc_start: 0.7522 (t-90) cc_final: 0.6934 (m170)
  outliers start: 13
  outliers final: 5
  residues processed: 64
  average time/residue: 0.6750
  time to fit residues: 44.6257
Evaluate side-chains
  64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  392 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    0.0000
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 327 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.141652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.107976 restraints weight = 4267.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.86
r_work: 0.3081 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4450  Z= 0.117
  Angle     :  0.480   8.761   6073  Z= 0.242
  Chirality :  0.041   0.136    726
  Planarity :  0.005   0.047    783
  Dihedral  : 10.315  85.310    676
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.47 %
    Favored  : 83.89 %
  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 are not related in a simple way.
  whole:  0.97 (0.36), residues: 565
  helix:  1.86 (0.31), residues: 287
  sheet: -1.49 (0.54), residues: 79
  loop : -0.12 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  62 
 TYR   0.007   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A   4 
 TRP   0.003   0.001   TRP A 525 
 HIS   0.012   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4450)
  covalent geometry    : angle       0.47992 ( 6073)
  hydrogen bonds       : bond        0.02939 (  222)
  hydrogen bonds       : angle       3.93917 (  645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1714.76 seconds
wall clock time: 30 minutes 6.61 seconds (1806.61 seconds total)