Starting phenix.real_space_refine
on Mon Jul 28 22:22:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2025/8zoy_60322_trim.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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
     P       1      5.49       5
     S      24      5.16       5
     Cl      1      4.86       5
     C    3568      2.51       5
     N     843      2.21       5
     O    1004      1.98       5
     H    5260      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10701
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8768
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 547, 8749
          Classifications: {'peptide': 547}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 527}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 547, 8749
          Classifications: {'peptide': 547}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 527}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 8870
    Chain: "B"
      Number of atoms: 1822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 1822
          Classifications: {'peptide': 119}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 103
          Unusual residues: {' CL': 1, 'LNR': 1, 'PTY': 1}
          Classifications: {'undetermined': 3, 'water': 62}
          Link IDs: {None: 64}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 22
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 101 " occ=0.45
      ... (36 atoms not shown)
      pdb=" HZ BPHE A 101 " occ=0.55
  Time building chain proxies: 9.91, per 1000 atoms: 0.93
  Number of scatterers: 10701
  At special positions: 0
  Unit cell: (96.6, 70.84, 97.52, 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)
     Cl      1     17.00
     S      24     16.00
     P       1     15.00
     O    1004      8.00
     N     843      7.00
     C    3568      6.00
     H    5260      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " 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
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1224

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      68.6% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 74
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.577A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 121
      Proline residue:  A  97  - end of helix
      removed outlier: 4.917A  pdb=" N   MET A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.605A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.756A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 218
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 263 through 267
    Processing helix  chain 'A' and resid 268 through 282
    Processing helix  chain 'A' and resid 286 through 295
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 4.449A  pdb=" N   TRP A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 372
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 4.588A  pdb=" N   ALA A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 385
      No H-bonds generated for 'chain 'A' and resid 383 through 385'
    Processing helix  chain 'A' and resid 386 through 398
      Proline residue:  A 392  - end of helix
      removed outlier: 3.634A  pdb=" N   THR A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.536A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 3.623A  pdb=" N   ARG A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 441 through 458
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.508A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 494
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.874A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 594 through 597
    Processing helix  chain 'A' and resid 598 through 604
      removed outlier: 4.091A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN A 603 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 616
      removed outlier: 4.013A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 5.912A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   SER B 119 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 119 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
      removed outlier: 5.912A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   SER B 119 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 119 " (cutoff:3.500A)

    339 hydrogen bonds defined for protein.
    958 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: 3.89

  Time building geometry restraints manager: 3.75 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5253
        1.03 -     1.23: 36
        1.23 -     1.42: 2436
        1.42 -     1.62: 3031
        1.62 -     1.81: 39
  Bond restraints: 10795
  Sorted by residual:
  bond pdb=" CAG LNR A 701 "
       pdb=" CAJ LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.384  1.525 -0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" CAF LNR A 701 "
       pdb=" CAK LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.386  1.522 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" CAE LNR A 701 "
       pdb=" CAI LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.384  1.519 -0.135 2.00e-02 2.50e+03 4.56e+01
  bond pdb=" CAI LNR A 701 "
       pdb=" CAJ LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.402  1.315  0.087 2.00e-02 2.50e+03 1.88e+01
  bond pdb=" CAE LNR A 701 "
       pdb=" CAF LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.392  1.308  0.084 2.00e-02 2.50e+03 1.77e+01
  ... (remaining 10790 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 18151
        1.19 -     2.39: 1163
        2.39 -     3.58: 59
        3.58 -     4.77: 28
        4.77 -     5.96: 5
  Bond angle restraints: 19406
  Sorted by residual:
  angle pdb=" N   ILE A 265 "
        pdb=" CA  ILE A 265 "
        pdb=" C   ILE A 265 "
      ideal   model   delta    sigma   weight residual
     111.62  108.26    3.36 7.90e-01 1.60e+00 1.81e+01
  angle pdb=" CA  PRO B  87 "
        pdb=" N   PRO B  87 "
        pdb=" CD  PRO B  87 "
      ideal   model   delta    sigma   weight residual
     112.00  107.29    4.71 1.40e+00 5.10e-01 1.13e+01
  angle pdb=" N   PRO B  87 "
        pdb=" CD  PRO B  87 "
        pdb=" CG  PRO B  87 "
      ideal   model   delta    sigma   weight residual
     103.20   98.68    4.52 1.50e+00 4.44e-01 9.09e+00
  angle pdb=" C   PRO A  83 "
        pdb=" N   TYR A  84 "
        pdb=" CA  TYR A  84 "
      ideal   model   delta    sigma   weight residual
     121.66  117.75    3.91 1.76e+00 3.23e-01 4.93e+00
  angle pdb=" CA  TYR A  84 "
        pdb=" CB  TYR A  84 "
        pdb=" CG  TYR A  84 "
      ideal   model   delta    sigma   weight residual
     113.90  117.82   -3.92 1.80e+00 3.09e-01 4.74e+00
  ... (remaining 19401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 4572
       16.02 -    32.04: 358
       32.04 -    48.06: 122
       48.06 -    64.08: 70
       64.08 -    80.09: 6
  Dihedral angle restraints: 5128
    sinusoidal: 2619
      harmonic: 2509
  Sorted by residual:
  dihedral pdb=" CA  TRP A 128 "
           pdb=" C   TRP A 128 "
           pdb=" N   LYS A 129 "
           pdb=" CA  LYS A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.79   18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ASP B  61 "
           pdb=" CB  ASP B  61 "
           pdb=" CG  ASP B  61 "
           pdb=" OD1 ASP B  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.96   56.96     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  PHE A 409 "
           pdb=" C   PHE A 409 "
           pdb=" N   VAL A 410 "
           pdb=" CA  VAL A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.51   15.49     0      5.00e+00 4.00e-02 9.59e+00
  ... (remaining 5125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 612
       0.043 -    0.086: 170
       0.086 -    0.129: 42
       0.129 -    0.172: 3
       0.172 -    0.214: 1
  Chirality restraints: 828
  Sorted by residual:
  chirality pdb=" CAL LNR A 701 "
            pdb=" CAH LNR A 701 "
            pdb=" CAK LNR A 701 "
            pdb=" OAD LNR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.50    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  PRO A  83 "
            pdb=" N   PRO A  83 "
            pdb=" C   PRO A  83 "
            pdb=" CB  PRO A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  PRO A 132 "
            pdb=" N   PRO A 132 "
            pdb=" C   PRO A 132 "
            pdb=" CB  PRO A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 825 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 102 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   LEU A 102 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LEU A 102 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ILE A 103 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  86 "   -0.052 5.00e-02 4.00e+02   7.60e-02 9.23e+00
        pdb=" N   PRO B  87 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B  87 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  87 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 214 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   TYR A 214 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TYR A 214 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 215 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 700
        2.20 -     2.80: 22286
        2.80 -     3.40: 32321
        3.40 -     4.00: 44441
        4.00 -     4.60: 67646
  Nonbonded interactions: 167394
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 298 "
            pdb=" H   ASP A 298 "
     model   vdw
     1.594 2.450
  nonbonded pdb=" HZ2 LYS A 522 "
            pdb=" O   ALA A 616 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" OE2 GLU B   6 "
            pdb=" H   CYS B  95 "
     model   vdw
     1.630 2.450
  nonbonded pdb="HE21 GLN A 234 "
            pdb=" OE1 GLN A 236 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" H   PHE A 335 "
            pdb=" OH  TYR B 107 "
     model   vdw
     1.635 2.450
  ... (remaining 167389 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.45 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:             1.420
  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:             0.190
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.380
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.050
  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:12.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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      :  0.007   0.141   5537  Z= 0.306
  Angle     :  0.647   5.963   7544  Z= 0.372
  Chirality :  0.042   0.214    828
  Planarity :  0.006   0.076    924
  Dihedral  : 15.324  80.094   1886
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.37 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.33), residues: 661
  helix:  0.80 (0.27), residues: 375
  sheet: -0.60 (0.78), residues: 33
  loop :  0.67 (0.43), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  80 
 HIS   0.005   0.001   HIS A 370 
 PHE   0.024   0.002   PHE A 316 
 TYR   0.021   0.002   TYR A 572 
 ARG   0.005   0.001   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14191 (  335)
  hydrogen bonds       : angle       6.88580 (  958)
  SS BOND              : bond        0.00432 (    2)
  SS BOND              : angle       1.49952 (    4)
  covalent geometry    : bond        0.00659 ( 5535)
  covalent geometry    : angle       0.64611 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7561 (mp0)
REVERT: A  607 ARG cc_start: 0.8065 (ptp-170) cc_final: 0.7803 (ptm160)
  outliers start: 6
  outliers final: 6
  residues processed: 88
  average time/residue: 2.3795
  time to fit residues: 220.3263
Evaluate side-chains
  87 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  350 ASN
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0670
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 436 GLN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119440 restraints weight = 18009.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.38
r_work: 0.3296 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5537  Z= 0.163
  Angle     :  0.546   5.166   7544  Z= 0.294
  Chirality :  0.038   0.132    828
  Planarity :  0.005   0.053    924
  Dihedral  :  8.238  79.700    761
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.73 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.34), residues: 661
  helix:  1.09 (0.26), residues: 381
  sheet: -0.45 (0.88), residues: 33
  loop :  0.82 (0.45), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.017   0.002   PHE A 316 
 TYR   0.017   0.002   TYR A  84 
 ARG   0.005   0.001   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04688 (  335)
  hydrogen bonds       : angle       5.56931 (  958)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       1.03295 (    4)
  covalent geometry    : bond        0.00356 ( 5535)
  covalent geometry    : angle       0.54589 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7050 (p0)
REVERT: A  303 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.7076 (mttm)
REVERT: A  304 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7866 (mp0)
REVERT: A  377 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8010 (pm20)
REVERT: A  607 ARG cc_start: 0.8127 (ptp-170) cc_final: 0.7882 (ptm160)
  outliers start: 9
  outliers final: 4
  residues processed: 93
  average time/residue: 2.3842
  time to fit residues: 233.1886
Evaluate side-chains
  93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   62 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119358 restraints weight = 18302.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.40
r_work: 0.3299 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5537  Z= 0.157
  Angle     :  0.523   4.853   7544  Z= 0.283
  Chirality :  0.038   0.134    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.999  76.808    753
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.26 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.34), residues: 661
  helix:  1.20 (0.27), residues: 381
  sheet: -0.25 (0.73), residues: 46
  loop :  0.97 (0.46), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 370 
 PHE   0.017   0.002   PHE A 316 
 TYR   0.015   0.002   TYR A  84 
 ARG   0.003   0.001   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  335)
  hydrogen bonds       : angle       5.36639 (  958)
  SS BOND              : bond        0.00301 (    2)
  SS BOND              : angle       1.18434 (    4)
  covalent geometry    : bond        0.00344 ( 5535)
  covalent geometry    : angle       0.52208 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7086 (mttm)
REVERT: A  304 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7853 (mp0)
REVERT: A  377 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8012 (pm20)
REVERT: A  607 ARG cc_start: 0.8173 (ptp-170) cc_final: 0.7968 (ptm160)
REVERT: B   83 ASN cc_start: 0.8665 (m-40) cc_final: 0.8387 (m-40)
  outliers start: 6
  outliers final: 4
  residues processed: 90
  average time/residue: 2.5922
  time to fit residues: 246.3588
Evaluate side-chains
  93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.122661 restraints weight = 16410.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.32
r_work: 0.3339 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5537  Z= 0.119
  Angle     :  0.487   4.931   7544  Z= 0.261
  Chirality :  0.037   0.131    828
  Planarity :  0.005   0.042    924
  Dihedral  :  6.689  75.454    753
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.90 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.34), residues: 661
  helix:  1.40 (0.27), residues: 382
  sheet: -0.76 (0.73), residues: 42
  loop :  0.93 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 316 
 TYR   0.015   0.001   TYR A  84 
 ARG   0.004   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  335)
  hydrogen bonds       : angle       5.06978 (  958)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.86474 (    4)
  covalent geometry    : bond        0.00252 ( 5535)
  covalent geometry    : angle       0.48627 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.7037 (mttm)
REVERT: A  304 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7845 (mp0)
REVERT: A  373 LYS cc_start: 0.8295 (mppt) cc_final: 0.8054 (mmmm)
REVERT: A  377 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (pm20)
REVERT: B   56 ILE cc_start: 0.8812 (mt) cc_final: 0.8578 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 89
  average time/residue: 2.2397
  time to fit residues: 210.1542
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119863 restraints weight = 17114.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.33
r_work: 0.3304 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5537  Z= 0.156
  Angle     :  0.507   4.877   7544  Z= 0.275
  Chirality :  0.038   0.133    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.707  73.584    751
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.08 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.34), residues: 661
  helix:  1.47 (0.27), residues: 378
  sheet: -0.10 (0.70), residues: 46
  loop :  0.96 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.017   0.002   PHE A 316 
 TYR   0.014   0.001   TYR A 391 
 ARG   0.003   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  335)
  hydrogen bonds       : angle       5.19560 (  958)
  SS BOND              : bond        0.00326 (    2)
  SS BOND              : angle       1.12196 (    4)
  covalent geometry    : bond        0.00346 ( 5535)
  covalent geometry    : angle       0.50682 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7055 (mttm)
REVERT: A  304 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7845 (mp0)
REVERT: A  373 LYS cc_start: 0.8311 (mppt) cc_final: 0.8045 (mmmm)
REVERT: A  377 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7977 (pm20)
REVERT: B   83 ASN cc_start: 0.8691 (m-40) cc_final: 0.8455 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 87
  average time/residue: 2.5964
  time to fit residues: 237.2881
Evaluate side-chains
  86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN
B  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117731 restraints weight = 23178.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.55
r_work: 0.3274 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5537  Z= 0.167
  Angle     :  0.517   5.037   7544  Z= 0.279
  Chirality :  0.038   0.134    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.712  72.666    751
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.62 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.34), residues: 661
  helix:  1.42 (0.27), residues: 378
  sheet: -0.55 (0.72), residues: 40
  loop :  0.86 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  80 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.018   0.002   PHE A 316 
 TYR   0.014   0.001   TYR A  84 
 ARG   0.003   0.001   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  335)
  hydrogen bonds       : angle       5.22748 (  958)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       1.18277 (    4)
  covalent geometry    : bond        0.00371 ( 5535)
  covalent geometry    : angle       0.51636 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  377 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7996 (pm20)
REVERT: B   83 ASN cc_start: 0.8715 (m-40) cc_final: 0.8468 (m-40)
  outliers start: 7
  outliers final: 3
  residues processed: 85
  average time/residue: 2.5991
  time to fit residues: 233.3535
Evaluate side-chains
  83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN
B  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119684 restraints weight = 16995.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.33
r_work: 0.3305 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5537  Z= 0.159
  Angle     :  0.511   5.188   7544  Z= 0.275
  Chirality :  0.038   0.134    828
  Planarity :  0.005   0.045    924
  Dihedral  :  6.604  71.890    751
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 15.15 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.34), residues: 661
  helix:  1.44 (0.27), residues: 378
  sheet: -0.51 (0.71), residues: 40
  loop :  0.84 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.017   0.002   PHE A 316 
 TYR   0.016   0.001   TYR A 391 
 ARG   0.003   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  335)
  hydrogen bonds       : angle       5.18375 (  958)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       1.11810 (    4)
  covalent geometry    : bond        0.00355 ( 5535)
  covalent geometry    : angle       0.51039 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A  377 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (pm20)
REVERT: B   83 ASN cc_start: 0.8686 (m-40) cc_final: 0.8448 (m-40)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 3.0566
  time to fit residues: 276.0146
Evaluate side-chains
  86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0870
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121648 restraints weight = 20425.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.47
r_work: 0.3325 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5537  Z= 0.116
  Angle     :  0.479   5.274   7544  Z= 0.256
  Chirality :  0.037   0.131    828
  Planarity :  0.005   0.043    924
  Dihedral  :  6.259  71.177    751
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.97 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.34), residues: 661
  helix:  1.58 (0.27), residues: 378
  sheet: -0.52 (0.69), residues: 42
  loop :  0.91 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 316 
 TYR   0.014   0.001   TYR A 391 
 ARG   0.002   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  335)
  hydrogen bonds       : angle       4.94672 (  958)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.81972 (    4)
  covalent geometry    : bond        0.00251 ( 5535)
  covalent geometry    : angle       0.47872 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7899 (mp0)
REVERT: A  377 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7961 (pm20)
REVERT: B   56 ILE cc_start: 0.8821 (mt) cc_final: 0.8588 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 2.0646
  time to fit residues: 187.6892
Evaluate side-chains
  83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   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 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.120334 restraints weight = 17251.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.34
r_work: 0.3313 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5537  Z= 0.149
  Angle     :  0.499   4.913   7544  Z= 0.270
  Chirality :  0.038   0.133    828
  Planarity :  0.005   0.045    924
  Dihedral  :  6.352  70.874    751
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 15.15 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.34), residues: 661
  helix:  1.56 (0.27), residues: 378
  sheet: -0.48 (0.69), residues: 42
  loop :  0.89 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 
 PHE   0.016   0.002   PHE A 316 
 TYR   0.015   0.001   TYR A 391 
 ARG   0.002   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  335)
  hydrogen bonds       : angle       5.08271 (  958)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       1.04655 (    4)
  covalent geometry    : bond        0.00329 ( 5535)
  covalent geometry    : angle       0.49851 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 1.408 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7878 (mp0)
REVERT: A  377 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (pm20)
  outliers start: 5
  outliers final: 3
  residues processed: 81
  average time/residue: 2.4538
  time to fit residues: 210.2966
Evaluate side-chains
  81 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 18 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0870
   chunk 15 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121794 restraints weight = 19725.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.44
r_work: 0.3327 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5537  Z= 0.117
  Angle     :  0.478   5.158   7544  Z= 0.256
  Chirality :  0.037   0.130    828
  Planarity :  0.005   0.043    924
  Dihedral  :  6.145  70.656    751
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 15.33 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.34), residues: 661
  helix:  1.55 (0.27), residues: 382
  sheet: -0.40 (0.69), residues: 42
  loop :  0.97 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 
 PHE   0.012   0.001   PHE A 316 
 TYR   0.015   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  335)
  hydrogen bonds       : angle       4.92458 (  958)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       0.80223 (    4)
  covalent geometry    : bond        0.00255 ( 5535)
  covalent geometry    : angle       0.47790 ( 7540)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7913 (mp0)
REVERT: A  377 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8033 (pm20)
REVERT: B   56 ILE cc_start: 0.8824 (mt) cc_final: 0.8597 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 2.6494
  time to fit residues: 229.0019
Evaluate side-chains
  83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0470
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 581 GLN
A 603 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.121483 restraints weight = 18371.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.39
r_work: 0.3325 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3222
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3222
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5537  Z= 0.129
  Angle     :  0.484   5.111   7544  Z= 0.261
  Chirality :  0.037   0.132    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.137  70.356    751
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 15.69 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.34), residues: 661
  helix:  1.57 (0.27), residues: 382
  sheet: -0.35 (0.69), residues: 42
  loop :  0.98 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 
 PHE   0.014   0.001   PHE A 316 
 TYR   0.013   0.001   TYR A 391 
 ARG   0.002   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  335)
  hydrogen bonds       : angle       4.95982 (  958)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.93206 (    4)
  covalent geometry    : bond        0.00283 ( 5535)
  covalent geometry    : angle       0.48404 ( 7540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9996.95 seconds
wall clock time: 179 minutes 24.31 seconds (10764.31 seconds total)