Starting phenix.real_space_refine
on Sat Oct 11 02:02:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zoy_60322/10_2025/8zoy_60322_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zoy_60322/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zoy_60322/10_2025/8zoy_60322_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zoy_60322/10_2025/8zoy_60322_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zoy_60322/10_2025/8zoy_60322.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zoy_60322/10_2025/8zoy_60322.map"
  }
  resolution = 2.5
  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=   0.024
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.65, per 1000 atoms: 0.34
  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: 0.78
  Conformation dependent library (CDL) restraints added in 423.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.28
  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: 2.54

  Time building geometry restraints manager: 1.07 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:             1.490
  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:             0.060
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.560
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (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
 ARG   0.005   0.001   ARG A 216 
 TYR   0.021   0.002   TYR A 572 
 PHE   0.024   0.002   PHE A 316 
 TRP   0.013   0.002   TRP A  80 
 HIS   0.005   0.001   HIS A 370 

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

*********************** 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  : 0.377 
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: 5
  residues processed: 88
  average time/residue: 1.2387
  time to fit residues: 113.9456
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  : 0.263 
-------------------------------------------------------------------------------
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  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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.141197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.117429 restraints weight = 18144.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.39
r_work: 0.3270 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5537  Z= 0.211
  Angle     :  0.577   5.226   7544  Z= 0.314
  Chirality :  0.040   0.137    828
  Planarity :  0.006   0.054    924
  Dihedral  :  8.576  79.309    759
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.90 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.34), residues: 661
  helix:  0.98 (0.26), residues: 380
  sheet: -0.56 (0.85), residues: 33
  loop :  0.79 (0.45), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 518 
 TYR   0.018   0.002   TYR A 572 
 PHE   0.021   0.002   PHE A 316 
 TRP   0.011   0.001   TRP A  80 
 HIS   0.004   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 5535)
  covalent geometry    : angle       0.57685 ( 7540)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       1.29012 (    4)
  hydrogen bonds       : bond        0.05158 (  335)
  hydrogen bonds       : angle       5.74690 (  958)

*********************** 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
  94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7851 (mp0)
REVERT: A  377 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8021 (pm20)
REVERT: A  607 ARG cc_start: 0.8188 (ptp-170) cc_final: 0.7951 (ptm160)
  outliers start: 9
  outliers final: 6
  residues processed: 90
  average time/residue: 1.2705
  time to fit residues: 119.3201
Evaluate side-chains
  91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  298 ASP
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   62 SER
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0050
   chunk 28 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.133508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.108065 restraints weight = 17963.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.46
r_work: 0.3078 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5537  Z= 0.119
  Angle     :  0.500   5.068   7544  Z= 0.267
  Chirality :  0.037   0.131    828
  Planarity :  0.005   0.041    924
  Dihedral  :  7.046  78.272    755
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.73 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.34), residues: 661
  helix:  1.30 (0.27), residues: 382
  sheet: -0.73 (0.76), residues: 40
  loop :  0.85 (0.45), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 518 
 TYR   0.015   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 408 
 TRP   0.009   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5535)
  covalent geometry    : angle       0.49938 ( 7540)
  SS BOND              : bond        0.00241 (    2)
  SS BOND              : angle       0.90184 (    4)
  hydrogen bonds       : bond        0.04069 (  335)
  hydrogen bonds       : angle       5.21641 (  958)

*********************** 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
  97 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7829 (mp0)
REVERT: A  377 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7789 (pm20)
REVERT: A  607 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7830 (ptm160)
REVERT: B   56 ILE cc_start: 0.8735 (mt) cc_final: 0.8456 (mp)
REVERT: B   83 ASN cc_start: 0.8559 (m-40) cc_final: 0.8250 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 94
  average time/residue: 1.1852
  time to fit residues: 116.7606
Evaluate side-chains
  90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.130716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.104305 restraints weight = 19309.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.54
r_work: 0.3033 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5537  Z= 0.162
  Angle     :  0.521   5.010   7544  Z= 0.282
  Chirality :  0.038   0.134    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.992  75.969    753
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.34), residues: 661
  helix:  1.29 (0.27), residues: 382
  sheet: -0.24 (0.72), residues: 46
  loop :  0.97 (0.46), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 216 
 TYR   0.014   0.001   TYR A 572 
 PHE   0.017   0.002   PHE A 316 
 TRP   0.009   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5535)
  covalent geometry    : angle       0.52056 ( 7540)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       1.18363 (    4)
  hydrogen bonds       : bond        0.04409 (  335)
  hydrogen bonds       : angle       5.28887 (  958)

*********************** 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
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7815 (mp0)
REVERT: A  377 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7771 (pm20)
REVERT: A  607 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7794 (ptm160)
REVERT: B   83 ASN cc_start: 0.8547 (m-40) cc_final: 0.8266 (m-40)
  outliers start: 8
  outliers final: 3
  residues processed: 89
  average time/residue: 1.1940
  time to fit residues: 111.3488
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  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain B residue   19 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.130487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.104747 restraints weight = 17276.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.45
r_work: 0.3039 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1364

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= 0.165
  Angle     :  0.517   5.166   7544  Z= 0.280
  Chirality :  0.038   0.135    828
  Planarity :  0.005   0.045    924
  Dihedral  :  6.876  74.063    751
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.34), residues: 661
  helix:  1.38 (0.27), residues: 378
  sheet: -0.58 (0.74), residues: 40
  loop :  0.83 (0.45), residues: 243

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5535)
  covalent geometry    : angle       0.51653 ( 7540)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       1.18429 (    4)
  hydrogen bonds       : bond        0.04375 (  335)
  hydrogen bonds       : angle       5.26706 (  958)

*********************** 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
  90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7817 (mp0)
REVERT: A  377 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7778 (pm20)
REVERT: A  607 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7789 (ptm160)
REVERT: B   83 ASN cc_start: 0.8589 (m-40) cc_final: 0.8307 (m-40)
  outliers start: 7
  outliers final: 4
  residues processed: 87
  average time/residue: 1.1327
  time to fit residues: 103.2640
Evaluate side-chains
  89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0470
   chunk 48 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.3678

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.134026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.107216 restraints weight = 21794.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.64
r_work: 0.3036 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5537  Z= 0.113
  Angle     :  0.479   5.150   7544  Z= 0.256
  Chirality :  0.037   0.130    828
  Planarity :  0.005   0.043    924
  Dihedral  :  6.396  73.497    751
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.08 %
    Favored  : 84.85 %
  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 aren not related in a simple way.
  whole:  1.64 (0.34), residues: 661
  helix:  1.55 (0.27), residues: 378
  sheet: -0.67 (0.71), residues: 42
  loop :  0.90 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 518 
 TYR   0.014   0.001   TYR A 391 
 PHE   0.012   0.001   PHE A 316 
 TRP   0.010   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5535)
  covalent geometry    : angle       0.47828 ( 7540)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       0.80358 (    4)
  hydrogen bonds       : bond        0.03812 (  335)
  hydrogen bonds       : angle       4.96238 (  958)

*********************** 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
  94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8391 (p) cc_final: 0.8162 (t)
REVERT: A  304 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7853 (mp0)
REVERT: A  377 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7714 (pm20)
REVERT: B   56 ILE cc_start: 0.8676 (mt) cc_final: 0.8381 (mp)
REVERT: B   83 ASN cc_start: 0.8519 (m-40) cc_final: 0.8244 (m-40)
  outliers start: 6
  outliers final: 4
  residues processed: 90
  average time/residue: 1.1384
  time to fit residues: 107.6907
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   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 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 = 0.3481 r_free = 0.3481 target = 0.132558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.106319 restraints weight = 18881.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.53
r_work: 0.3024 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5537  Z= 0.136
  Angle     :  0.494   5.013   7544  Z= 0.265
  Chirality :  0.037   0.132    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.372  73.037    751
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.34), residues: 661
  helix:  1.59 (0.27), residues: 378
  sheet: -0.40 (0.71), residues: 40
  loop :  0.89 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 216 
 TYR   0.013   0.001   TYR A  84 
 PHE   0.015   0.001   PHE A 316 
 TRP   0.009   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5535)
  covalent geometry    : angle       0.49317 ( 7540)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       1.00484 (    4)
  hydrogen bonds       : bond        0.04033 (  335)
  hydrogen bonds       : angle       5.03420 (  958)

*********************** 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
  90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8414 (p) cc_final: 0.8185 (t)
REVERT: A  304 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7835 (mp0)
REVERT: A  377 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7729 (pm20)
REVERT: B   83 ASN cc_start: 0.8514 (m-40) cc_final: 0.8255 (m-40)
  outliers start: 6
  outliers final: 3
  residues processed: 87
  average time/residue: 1.2093
  time to fit residues: 110.0292
Evaluate side-chains
  85 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.132467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.106581 restraints weight = 17868.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.49
r_work: 0.3033 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5537  Z= 0.137
  Angle     :  0.491   4.959   7544  Z= 0.264
  Chirality :  0.037   0.132    828
  Planarity :  0.005   0.043    924
  Dihedral  :  6.318  72.633    751
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.34), residues: 661
  helix:  1.51 (0.27), residues: 382
  sheet: -0.34 (0.70), residues: 40
  loop :  0.97 (0.45), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 216 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.015   0.001   PHE A 316 
 TRP   0.012   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5535)
  covalent geometry    : angle       0.49031 ( 7540)
  SS BOND              : bond        0.00293 (    2)
  SS BOND              : angle       0.98792 (    4)
  hydrogen bonds       : bond        0.04035 (  335)
  hydrogen bonds       : angle       5.02967 (  958)

*********************** 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
  85 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8404 (p) cc_final: 0.8175 (t)
REVERT: A  304 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7812 (mp0)
REVERT: A  377 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7732 (pm20)
REVERT: B   56 ILE cc_start: 0.8706 (mt) cc_final: 0.8406 (mp)
REVERT: B   83 ASN cc_start: 0.8514 (m-40) cc_final: 0.8267 (m-40)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 1.2846
  time to fit residues: 111.3052
Evaluate side-chains
  85 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3467 r_free = 0.3467 target = 0.131336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.104729 restraints weight = 20007.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.57
r_work: 0.3019 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5537  Z= 0.156
  Angle     :  0.505   4.936   7544  Z= 0.273
  Chirality :  0.038   0.132    828
  Planarity :  0.005   0.044    924
  Dihedral  :  6.403  72.158    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 :  0.71 %
    Allowed  : 15.51 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.34), residues: 661
  helix:  1.48 (0.27), residues: 382
  sheet: -0.29 (0.70), residues: 40
  loop :  0.96 (0.45), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 216 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.017   0.002   PHE A 316 
 TRP   0.010   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5535)
  covalent geometry    : angle       0.50426 ( 7540)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       1.11024 (    4)
  hydrogen bonds       : bond        0.04225 (  335)
  hydrogen bonds       : angle       5.12332 (  958)

*********************** 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
  85 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8436 (p) cc_final: 0.8208 (t)
REVERT: A  304 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7847 (mp0)
REVERT: A  377 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7800 (pm20)
REVERT: B   83 ASN cc_start: 0.8546 (m-40) cc_final: 0.8281 (m-40)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 1.3005
  time to fit residues: 112.6637
Evaluate side-chains
  82 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
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 52 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0020
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.132879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.106054 restraints weight = 21061.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.61
r_work: 0.3011 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1730

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= 0.127
  Angle     :  0.486   5.115   7544  Z= 0.261
  Chirality :  0.037   0.131    828
  Planarity :  0.005   0.048    924
  Dihedral  :  6.261  72.045    751
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.34), residues: 661
  helix:  1.50 (0.27), residues: 382
  sheet: -0.45 (0.69), residues: 42
  loop :  0.99 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 216 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.014   0.001   PHE A 501 
 TRP   0.013   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5535)
  covalent geometry    : angle       0.48568 ( 7540)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       0.90002 (    4)
  hydrogen bonds       : bond        0.03959 (  335)
  hydrogen bonds       : angle       5.00433 (  958)

********************** 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
  83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8458 (p) cc_final: 0.8205 (t)
REVERT: A  304 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7844 (mp0)
REVERT: A  377 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7812 (pm20)
  outliers start: 4
  outliers final: 3
  residues processed: 81
  average time/residue: 1.2161
  time to fit residues: 103.1118
Evaluate side-chains
  82 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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 37 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 50 optimal weight:    0.2980
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.133528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.107672 restraints weight = 18036.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.49
r_work: 0.3043 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1777

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= 0.121
  Angle     :  0.481   5.100   7544  Z= 0.259
  Chirality :  0.037   0.131    828
  Planarity :  0.005   0.045    924
  Dihedral  :  6.169  71.897    751
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 15.86 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.34), residues: 661
  helix:  1.57 (0.27), residues: 382
  sheet: -0.42 (0.70), residues: 42
  loop :  0.98 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 216 
 TYR   0.014   0.001   TYR A 271 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.015   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5535)
  covalent geometry    : angle       0.48116 ( 7540)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       0.87798 (    4)
  hydrogen bonds       : bond        0.03879 (  335)
  hydrogen bonds       : angle       4.94968 (  958)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4890.47 seconds
wall clock time: 83 minutes 26.21 seconds (5006.21 seconds total)