Starting phenix.real_space_refine
on Fri Jun 13 11:28:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r22_18833/06_2025/8r22_18833.cif"
  }
  resolution = 3.9
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S     106      5.16       5
     C    9620      2.51       5
     N    2556      2.21       5
     O    2786      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 83 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15069
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5404
          Classifications: {'peptide': 710}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 667}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 3454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3454
          Classifications: {'peptide': 451}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 4, 'PTRANS': 31, 'TRANS': 415}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "C"
      Number of atoms: 3447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3447
          Classifications: {'peptide': 436}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 416}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 2763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2763
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 329}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   PRO A 492 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CD  PRO A 492 " occ=0.25
  Time building chain proxies: 8.45, per 1000 atoms: 0.56
  Number of scatterers: 15069
  At special positions: 0
  Unit cell: (133.32, 124.08, 133.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S     106     16.00
     O    2786      8.00
     N    2556      7.00
     C    9620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.59
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 800 "
        pdb="ZN    ZN C 800 " - pdb=" ND1 HIS C  70 "
        pdb="ZN    ZN C 800 " - pdb=" NE2 HIS C  68 "
        pdb="ZN    ZN C 800 " - pdb=" NE2 HIS C 157 "


  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3664

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      36.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 17
      removed outlier: 3.994A  pdb=" N   VAL A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 39
    Processing helix  chain 'A' and resid 46 through 51
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 73 through 83
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 99 through 103
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 134 through 139
    Processing helix  chain 'A' and resid 146 through 152
    Processing helix  chain 'A' and resid 158 through 175
    Processing helix  chain 'A' and resid 193 through 205
    Processing helix  chain 'A' and resid 211 through 224
    Processing helix  chain 'A' and resid 231 through 247
      removed outlier: 3.522A  pdb=" N   ALA A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      Proline residue:  A 242  - end of helix
    Processing helix  chain 'A' and resid 258 through 267
    Processing helix  chain 'A' and resid 279 through 289
    Processing helix  chain 'A' and resid 295 through 303
    Processing helix  chain 'A' and resid 310 through 329
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 358 through 375
    Processing helix  chain 'A' and resid 388 through 402
    Processing helix  chain 'A' and resid 410 through 418
    Processing helix  chain 'A' and resid 424 through 435
    Processing helix  chain 'A' and resid 443 through 457
    Processing helix  chain 'A' and resid 464 through 478
    Processing helix  chain 'A' and resid 494 through 508
      Proline residue:  A 503  - end of helix
    Processing helix  chain 'A' and resid 514 through 530
    Processing helix  chain 'A' and resid 535 through 543
    Processing helix  chain 'A' and resid 546 through 552
    Processing helix  chain 'A' and resid 559 through 575
    Processing helix  chain 'A' and resid 590 through 601
      removed outlier: 4.029A  pdb=" N   GLU A 595 " --> pdb=" O   SER A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 621
    Processing helix  chain 'A' and resid 631 through 642
    Processing helix  chain 'A' and resid 650 through 665
    Processing helix  chain 'A' and resid 688 through 697
    Processing helix  chain 'A' and resid 700 through 708
    Processing helix  chain 'A' and resid 713 through 733
    Processing helix  chain 'A' and resid 769 through 778
    Processing helix  chain 'A' and resid 781 through 788
    Processing helix  chain 'A' and resid 799 through 808
    Processing helix  chain 'B' and resid 110 through 115
    Processing helix  chain 'B' and resid 127 through 145
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 184 through 192
    Processing helix  chain 'B' and resid 274 through 289
    Processing helix  chain 'B' and resid 304 through 318
    Processing helix  chain 'B' and resid 333 through 341
    Processing helix  chain 'B' and resid 383 through 386
      No H-bonds generated for 'chain 'B' and resid 383 through 386'
    Processing helix  chain 'B' and resid 404 through 412
    Processing helix  chain 'B' and resid 429 through 433
    Processing helix  chain 'B' and resid 454 through 464
    Processing helix  chain 'C' and resid 57 through 60
      No H-bonds generated for 'chain 'C' and resid 57 through 60'
    Processing helix  chain 'C' and resid 77 through 78
      No H-bonds generated for 'chain 'C' and resid 77 through 78'
    Processing helix  chain 'C' and resid 94 through 113
      Proline residue:  C 101  - end of helix
    Processing helix  chain 'C' and resid 123 through 130
    Processing helix  chain 'C' and resid 214 through 231
      removed outlier: 3.502A  pdb=" N   ARG C 231 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 259
    Processing helix  chain 'C' and resid 275 through 280
    Processing helix  chain 'C' and resid 332 through 339
    Processing helix  chain 'C' and resid 359 through 363
    Processing helix  chain 'C' and resid 395 through 405
    Processing helix  chain 'C' and resid 420 through 431
      removed outlier: 4.585A  pdb=" N   GLN C 425 " --> pdb=" O   GLU C 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 14
      removed outlier: 3.896A  pdb=" N   ARG D  13 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1314 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: 3.12

  Time building geometry restraints manager: 4.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4906
        1.34 -     1.46: 2973
        1.46 -     1.58: 7381
        1.58 -     1.69: 0
        1.69 -     1.81: 151
  Bond restraints: 15411
  Sorted by residual:
  bond pdb=" C   HIS B 246 "
       pdb=" N   PRO B 247 "
    ideal  model  delta    sigma   weight residual
    1.326  1.357 -0.030 1.44e-02 4.82e+03 4.47e+00
  bond pdb=" C   ASP D 339 "
       pdb=" N   PRO D 340 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.87e+00
  bond pdb=" CG  PRO B 390 "
       pdb=" CD  PRO B 390 "
    ideal  model  delta    sigma   weight residual
    1.512  1.482  0.030 2.70e-02 1.37e+03 1.20e+00
  bond pdb=" C   GLY C 156 "
       pdb=" O   GLY C 156 "
    ideal  model  delta    sigma   weight residual
    1.237  1.231  0.006 7.00e-03 2.04e+04 8.33e-01
  bond pdb=" CG  LEU A 509 "
       pdb=" CD2 LEU A 509 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.32e-01
  ... (remaining 15406 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 20688
        2.45 -     4.89: 252
        4.89 -     7.34: 19
        7.34 -     9.79: 1
        9.79 -    12.23: 1
  Bond angle restraints: 20961
  Sorted by residual:
  angle pdb=" N   THR C 324 "
        pdb=" CA  THR C 324 "
        pdb=" C   THR C 324 "
      ideal   model   delta    sigma   weight residual
     109.30  116.38   -7.08 1.49e+00 4.50e-01 2.26e+01
  angle pdb=" C   ALA C 323 "
        pdb=" N   THR C 324 "
        pdb=" CA  THR C 324 "
      ideal   model   delta    sigma   weight residual
     122.59  117.73    4.86 1.11e+00 8.12e-01 1.92e+01
  angle pdb=" C   ASP C  14 "
        pdb=" N   VAL C  15 "
        pdb=" CA  VAL C  15 "
      ideal   model   delta    sigma   weight residual
     120.62  125.71   -5.09 1.64e+00 3.72e-01 9.61e+00
  angle pdb=" C   GLY B 396 "
        pdb=" N   HIS B 397 "
        pdb=" CA  HIS B 397 "
      ideal   model   delta    sigma   weight residual
     120.69  111.57    9.12 2.95e+00 1.15e-01 9.56e+00
  angle pdb=" C   ALA B 109 "
        pdb=" N   LEU B 110 "
        pdb=" CA  LEU B 110 "
      ideal   model   delta    sigma   weight residual
     119.78  123.27   -3.49 1.24e+00 6.50e-01 7.91e+00
  ... (remaining 20956 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 8271
       17.93 -    35.87: 797
       35.87 -    53.80: 140
       53.80 -    71.73: 24
       71.73 -    89.67: 13
  Dihedral angle restraints: 9245
    sinusoidal: 3606
      harmonic: 5639
  Sorted by residual:
  dihedral pdb=" CA  GLU C 301 "
           pdb=" C   GLU C 301 "
           pdb=" N   PHE C 302 "
           pdb=" CA  PHE C 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.62  -24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ALA A 255 "
           pdb=" C   ALA A 255 "
           pdb=" N   ALA A 256 "
           pdb=" CA  ALA A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.61   23.39     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  SER B 223 "
           pdb=" C   SER B 223 "
           pdb=" N   ASN B 224 "
           pdb=" CA  ASN B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 9242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1393
       0.032 -    0.063: 701
       0.063 -    0.095: 204
       0.095 -    0.127: 101
       0.127 -    0.158: 17
  Chirality restraints: 2416
  Sorted by residual:
  chirality pdb=" CA  VAL C 144 "
            pdb=" N   VAL C 144 "
            pdb=" C   VAL C 144 "
            pdb=" CB  VAL C 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  VAL D 300 "
            pdb=" N   VAL D 300 "
            pdb=" C   VAL D 300 "
            pdb=" CB  VAL D 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  ILE C  90 "
            pdb=" N   ILE C  90 "
            pdb=" C   ILE C  90 "
            pdb=" CB  ILE C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 2413 not shown)

  Planarity restraints: 2682
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 502 "   -0.037 5.00e-02 4.00e+02   5.61e-02 5.04e+00
        pdb=" N   PRO A 503 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 503 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 503 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 283 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO C 284 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 284 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 284 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 105 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 106 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 106 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 106 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2679 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 237
        2.66 -     3.22: 14639
        3.22 -     3.78: 22022
        3.78 -     4.34: 29848
        4.34 -     4.90: 49367
  Nonbonded interactions: 116113
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 178 "
            pdb="ZN    ZN C 800 "
     model   vdw
     2.098 2.230
  nonbonded pdb=" OH  TYR B 327 "
            pdb=" O   ASP B 386 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O   LEU D 155 "
            pdb=" OG  SER D 172 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OE1 GLN D 301 "
            pdb=" OH  TYR D 303 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG1 THR D 282 "
            pdb=" NE2 HIS D 347 "
     model   vdw
     2.177 3.120
  ... (remaining 116108 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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     34.420
  Find NCS groups from input model:        0.320
  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:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
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      :  0.005   0.232  15414  Z= 0.204
  Angle     :  0.673  12.234  20961  Z= 0.365
  Chirality :  0.044   0.158   2416
  Planarity :  0.005   0.056   2682
  Dihedral  : 14.653  89.667   5581
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -4.23 (0.16), residues: 1910
  helix: -1.69 (0.16), residues: 793
  sheet: -3.14 (0.26), residues: 263
  loop : -3.82 (0.18), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D   7 
 HIS   0.005   0.001   HIS D 347 
 PHE   0.029   0.002   PHE B 509 
 TYR   0.023   0.002   TYR C 278 
 ARG   0.004   0.000   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07280 (  438)
  hydrogen bonds       : angle       4.48733 ( 1314)
  metal coordination   : bond        0.20474 (    3)
  covalent geometry    : bond        0.00417 (15411)
  covalent geometry    : angle       0.67337 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 GLU cc_start: 0.7851 (tt0) cc_final: 0.7478 (tm-30)
REVERT: A  578 HIS cc_start: 0.7114 (m-70) cc_final: 0.6818 (m170)
REVERT: A  657 LEU cc_start: 0.9093 (tp) cc_final: 0.8890 (tp)
REVERT: A  781 LEU cc_start: 0.8420 (mm) cc_final: 0.8092 (mm)
REVERT: B   93 LEU cc_start: 0.6701 (tp) cc_final: 0.6422 (tt)
REVERT: B  184 MET cc_start: 0.7778 (mmm) cc_final: 0.7466 (mmm)
REVERT: B  409 MET cc_start: 0.8914 (mtp) cc_final: 0.8690 (ttm)
REVERT: C   30 MET cc_start: 0.8853 (ttm) cc_final: 0.8626 (ttm)
REVERT: C   44 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7624 (ptt-90)
REVERT: C   50 TYR cc_start: 0.6388 (m-80) cc_final: 0.6109 (m-80)
REVERT: C   62 ASP cc_start: 0.7928 (m-30) cc_final: 0.7719 (m-30)
REVERT: C  130 MET cc_start: 0.8573 (mmp) cc_final: 0.8349 (mmp)
REVERT: C  378 LEU cc_start: 0.6495 (tp) cc_final: 0.6150 (tt)
REVERT: D  211 PRO cc_start: 0.2871 (Cg_endo) cc_final: 0.2541 (Cg_exo)
REVERT: D  362 ASN cc_start: 0.8364 (p0) cc_final: 0.7966 (p0)
REVERT: D  363 ASP cc_start: 0.6189 (t0) cc_final: 0.5683 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2640
  time to fit residues: 87.9663
Evaluate side-chains
  156 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 163 optimal weight:    8.9990
   chunk 147 optimal weight:    8.9990
   chunk 81 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 152 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 176 optimal weight:   10.0000
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
A 578 HIS
A 653 GLN
A 767 GLN
B  15 ASN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 GLN
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 GLN
C  13 GLN
C 119 ASN
C 124 GLN
C 137 HIS
C 198 ASN
C 429 GLN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 112 GLN
D 367 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.107818 restraints weight = 25741.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.107734 restraints weight = 37410.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108409 restraints weight = 36846.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15414  Z= 0.127
  Angle     :  0.587   9.751  20961  Z= 0.295
  Chirality :  0.043   0.147   2416
  Planarity :  0.005   0.062   2682
  Dihedral  :  4.838  21.457   2063
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.06 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -2.81 (0.18), residues: 1910
  helix: -0.30 (0.18), residues: 801
  sheet: -2.47 (0.27), residues: 273
  loop : -3.27 (0.19), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 283 
 HIS   0.006   0.001   HIS D 347 
 PHE   0.021   0.001   PHE C 312 
 TYR   0.023   0.001   TYR C 107 
 ARG   0.004   0.000   ARG A 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  438)
  hydrogen bonds       : angle       3.90221 ( 1314)
  metal coordination   : bond        0.00731 (    3)
  covalent geometry    : bond        0.00294 (15411)
  covalent geometry    : angle       0.58702 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 1.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 GLU cc_start: 0.7906 (tt0) cc_final: 0.7389 (tm-30)
REVERT: B   32 MET cc_start: 0.7612 (mtm) cc_final: 0.7329 (mtm)
REVERT: B  206 PHE cc_start: 0.6082 (m-80) cc_final: 0.5816 (m-80)
REVERT: C   30 MET cc_start: 0.8774 (ttm) cc_final: 0.8554 (ttm)
REVERT: C   50 TYR cc_start: 0.6342 (m-80) cc_final: 0.6122 (m-80)
REVERT: C   56 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.8096 (ptt90)
REVERT: C   62 ASP cc_start: 0.7966 (m-30) cc_final: 0.7711 (m-30)
REVERT: C  265 ILE cc_start: 0.9063 (mm) cc_final: 0.8852 (mt)
REVERT: C  378 LEU cc_start: 0.6708 (tp) cc_final: 0.6343 (tt)
REVERT: C  382 MET cc_start: 0.8739 (ptm) cc_final: 0.8533 (ptp)
REVERT: D  202 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5945 (mt)
REVERT: D  249 ARG cc_start: 0.6354 (ttt90) cc_final: 0.6013 (ptm-80)
REVERT: D  362 ASN cc_start: 0.8358 (p0) cc_final: 0.7955 (p0)
REVERT: D  363 ASP cc_start: 0.6272 (t0) cc_final: 0.5745 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 202
  average time/residue: 0.2465
  time to fit residues: 76.9921
Evaluate side-chains
  166 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  176 ASP
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  367 HIS
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 160 optimal weight:    5.9990
   chunk 188 optimal weight:    6.9990
   chunk 122 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 185 optimal weight:    0.0170
   chunk 172 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 189 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 ASN
C 119 ASN
D  49 ASN
D 367 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.107988 restraints weight = 25174.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.106967 restraints weight = 36342.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.108280 restraints weight = 31156.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15414  Z= 0.114
  Angle     :  0.558   8.441  20961  Z= 0.280
  Chirality :  0.042   0.147   2416
  Planarity :  0.005   0.057   2682
  Dihedral  :  4.542  20.912   2063
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.35 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -2.07 (0.19), residues: 1910
  helix:  0.38 (0.18), residues: 807
  sheet: -2.00 (0.29), residues: 249
  loop : -3.00 (0.20), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 283 
 HIS   0.005   0.001   HIS D 367 
 PHE   0.014   0.001   PHE B 509 
 TYR   0.018   0.001   TYR C 107 
 ARG   0.004   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  438)
  hydrogen bonds       : angle       3.61037 ( 1314)
  metal coordination   : bond        0.00308 (    3)
  covalent geometry    : bond        0.00264 (15411)
  covalent geometry    : angle       0.55830 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 1.633 
Fit side-chains
REVERT: A  264 LEU cc_start: 0.8744 (tp) cc_final: 0.8479 (mt)
REVERT: A  373 GLU cc_start: 0.7839 (tt0) cc_final: 0.7343 (tm-30)
REVERT: A  454 LEU cc_start: 0.9212 (tp) cc_final: 0.8812 (tt)
REVERT: B   27 ASP cc_start: 0.7030 (m-30) cc_final: 0.6707 (m-30)
REVERT: B   32 MET cc_start: 0.7615 (mtm) cc_final: 0.7294 (mtm)
REVERT: B  287 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8673 (tp)
REVERT: B  486 MET cc_start: 0.7382 (mtm) cc_final: 0.6935 (tpt)
REVERT: B  500 ARG cc_start: 0.7183 (ttt180) cc_final: 0.6936 (ttt180)
REVERT: C   56 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.8028 (ptt90)
REVERT: C   62 ASP cc_start: 0.7811 (m-30) cc_final: 0.7570 (m-30)
REVERT: C  208 THR cc_start: 0.8592 (p) cc_final: 0.8189 (p)
REVERT: C  378 LEU cc_start: 0.6653 (tp) cc_final: 0.6266 (tt)
REVERT: D  202 LEU cc_start: 0.6150 (mt) cc_final: 0.5917 (mt)
REVERT: D  214 ASN cc_start: 0.5413 (t0) cc_final: 0.5172 (t0)
REVERT: D  241 ILE cc_start: 0.7497 (mp) cc_final: 0.7156 (mp)
REVERT: D  249 ARG cc_start: 0.6288 (ttt90) cc_final: 0.5776 (ptm-80)
REVERT: D  362 ASN cc_start: 0.8329 (p0) cc_final: 0.7928 (p0)
REVERT: D  363 ASP cc_start: 0.6317 (t0) cc_final: 0.5780 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 192
  average time/residue: 0.2526
  time to fit residues: 72.9979
Evaluate side-chains
  170 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 189 optimal weight:    0.3980
   chunk 102 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 138 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 168 optimal weight:    6.9990
   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 219 ASN
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 ASN
D 367 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.135933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107821 restraints weight = 25560.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.107556 restraints weight = 38513.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.108860 restraints weight = 37937.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15414  Z= 0.110
  Angle     :  0.534   7.637  20961  Z= 0.266
  Chirality :  0.041   0.145   2416
  Planarity :  0.004   0.046   2682
  Dihedral  :  4.346  20.127   2063
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.90 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -1.63 (0.19), residues: 1910
  helix:  0.75 (0.19), residues: 809
  sheet: -1.61 (0.31), residues: 245
  loop : -2.82 (0.20), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 283 
 HIS   0.007   0.001   HIS C 157 
 PHE   0.013   0.001   PHE B 509 
 TYR   0.023   0.001   TYR C 107 
 ARG   0.003   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (  438)
  hydrogen bonds       : angle       3.49307 ( 1314)
  metal coordination   : bond        0.00201 (    3)
  covalent geometry    : bond        0.00259 (15411)
  covalent geometry    : angle       0.53424 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 179
  time to evaluate  : 1.788 
Fit side-chains
REVERT: A  264 LEU cc_start: 0.8681 (tp) cc_final: 0.8467 (mp)
REVERT: A  373 GLU cc_start: 0.7768 (tt0) cc_final: 0.7219 (tm-30)
REVERT: A  454 LEU cc_start: 0.9162 (tp) cc_final: 0.8759 (tt)
REVERT: B   27 ASP cc_start: 0.7082 (m-30) cc_final: 0.6776 (m-30)
REVERT: B   93 LEU cc_start: 0.6039 (tt) cc_final: 0.5773 (tt)
REVERT: B  486 MET cc_start: 0.7433 (mtm) cc_final: 0.6919 (tpt)
REVERT: C    5 ARG cc_start: 0.7399 (mtt90) cc_final: 0.7168 (mtm110)
REVERT: C   62 ASP cc_start: 0.7788 (m-30) cc_final: 0.7533 (m-30)
REVERT: C  208 THR cc_start: 0.8652 (p) cc_final: 0.8250 (p)
REVERT: C  273 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.5285 (mp0)
REVERT: C  278 TYR cc_start: 0.5586 (p90) cc_final: 0.4929 (p90)
REVERT: C  378 LEU cc_start: 0.6377 (tp) cc_final: 0.5975 (tt)
REVERT: D  202 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5888 (mt)
REVERT: D  241 ILE cc_start: 0.7419 (mp) cc_final: 0.7086 (mp)
REVERT: D  249 ARG cc_start: 0.6393 (ttt90) cc_final: 0.6121 (ptm-80)
REVERT: D  362 ASN cc_start: 0.8342 (p0) cc_final: 0.7917 (p0)
REVERT: D  363 ASP cc_start: 0.6394 (t0) cc_final: 0.5882 (t0)
  outliers start: 35
  outliers final: 21
  residues processed: 208
  average time/residue: 0.2620
  time to fit residues: 82.0553
Evaluate side-chains
  187 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 1.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   49 ASN
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 191 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 121 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9980
   chunk 145 optimal weight:    0.1980
   chunk 135 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0970
   chunk 122 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.109958 restraints weight = 25368.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108827 restraints weight = 39955.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109930 restraints weight = 36218.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15414  Z= 0.099
  Angle     :  0.534   8.446  20961  Z= 0.263
  Chirality :  0.040   0.145   2416
  Planarity :  0.004   0.045   2682
  Dihedral  :  4.206  19.627   2063
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.26 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -1.31 (0.20), residues: 1910
  helix:  1.00 (0.19), residues: 809
  sheet: -1.38 (0.31), residues: 256
  loop : -2.68 (0.20), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 283 
 HIS   0.008   0.001   HIS C 157 
 PHE   0.013   0.001   PHE B 509 
 TYR   0.030   0.001   TYR C 107 
 ARG   0.004   0.000   ARG C 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02896 (  438)
  hydrogen bonds       : angle       3.38441 ( 1314)
  metal coordination   : bond        0.00174 (    3)
  covalent geometry    : bond        0.00229 (15411)
  covalent geometry    : angle       0.53414 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 180
  time to evaluate  : 1.645 
Fit side-chains
REVERT: A  373 GLU cc_start: 0.7776 (tt0) cc_final: 0.7344 (tm-30)
REVERT: A  454 LEU cc_start: 0.9146 (tp) cc_final: 0.8743 (tt)
REVERT: B   27 ASP cc_start: 0.7055 (m-30) cc_final: 0.6752 (m-30)
REVERT: B  486 MET cc_start: 0.7339 (mtm) cc_final: 0.7010 (tpt)
REVERT: C    5 ARG cc_start: 0.7320 (mtt90) cc_final: 0.7106 (mtm110)
REVERT: C   56 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7846 (ptt90)
REVERT: C  208 THR cc_start: 0.8439 (p) cc_final: 0.8053 (p)
REVERT: C  259 MET cc_start: 0.7637 (mmm) cc_final: 0.7413 (mmm)
REVERT: C  273 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5267 (mp0)
REVERT: C  278 TYR cc_start: 0.5601 (p90) cc_final: 0.4953 (p90)
REVERT: D  202 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5682 (mt)
REVERT: D  241 ILE cc_start: 0.7302 (mp) cc_final: 0.6981 (mp)
REVERT: D  362 ASN cc_start: 0.8273 (p0) cc_final: 0.7845 (p0)
REVERT: D  363 ASP cc_start: 0.6253 (t0) cc_final: 0.5715 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 205
  average time/residue: 0.2569
  time to fit residues: 79.4997
Evaluate side-chains
  185 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 152 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 193 optimal weight:    2.9990
   chunk 178 optimal weight:    9.9990
   chunk 145 optimal weight:    3.9990
   chunk 116 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 190 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 335 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.135689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.107192 restraints weight = 25452.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.107593 restraints weight = 37725.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108460 restraints weight = 36479.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15414  Z= 0.161
  Angle     :  0.579   7.707  20961  Z= 0.288
  Chirality :  0.042   0.154   2416
  Planarity :  0.005   0.045   2682
  Dihedral  :  4.340  20.261   2063
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.22 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -1.33 (0.19), residues: 1910
  helix:  0.95 (0.19), residues: 814
  sheet: -1.59 (0.31), residues: 255
  loop : -2.60 (0.20), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP D 283 
 HIS   0.009   0.001   HIS C 157 
 PHE   0.014   0.001   PHE B 509 
 TYR   0.031   0.001   TYR C 107 
 ARG   0.005   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  438)
  hydrogen bonds       : angle       3.55344 ( 1314)
  metal coordination   : bond        0.00351 (    3)
  covalent geometry    : bond        0.00387 (15411)
  covalent geometry    : angle       0.57904 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 1.656 
Fit side-chains
REVERT: A  373 GLU cc_start: 0.7948 (tt0) cc_final: 0.7339 (tm-30)
REVERT: B   27 ASP cc_start: 0.7261 (m-30) cc_final: 0.6968 (m-30)
REVERT: B  486 MET cc_start: 0.7596 (mtm) cc_final: 0.7033 (tpt)
REVERT: C    5 ARG cc_start: 0.7427 (mtt90) cc_final: 0.7168 (mtm110)
REVERT: C  208 THR cc_start: 0.8486 (p) cc_final: 0.8080 (p)
REVERT: C  259 MET cc_start: 0.7544 (mmm) cc_final: 0.7342 (mmm)
REVERT: C  273 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5293 (mp0)
REVERT: C  278 TYR cc_start: 0.5635 (p90) cc_final: 0.4863 (p90)
REVERT: C  378 LEU cc_start: 0.6383 (tp) cc_final: 0.5945 (tt)
REVERT: D  207 GLN cc_start: 0.6790 (tm-30) cc_final: 0.6429 (tm-30)
REVERT: D  241 ILE cc_start: 0.7442 (mp) cc_final: 0.7131 (mp)
REVERT: D  362 ASN cc_start: 0.8356 (p0) cc_final: 0.7950 (p0)
REVERT: D  363 ASP cc_start: 0.6380 (t0) cc_final: 0.5823 (t0)
  outliers start: 38
  outliers final: 30
  residues processed: 188
  average time/residue: 0.2356
  time to fit residues: 68.4387
Evaluate side-chains
  178 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  302 PHE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  176 ASP
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 176 optimal weight:    7.9990
   chunk 87 optimal weight:    0.1980
   chunk 161 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 160 optimal weight:    0.9980
   chunk 186 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0370
   chunk 59 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.138299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.110128 restraints weight = 25222.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.109588 restraints weight = 33358.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110622 restraints weight = 37044.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15414  Z= 0.098
  Angle     :  0.526   7.536  20961  Z= 0.260
  Chirality :  0.040   0.143   2416
  Planarity :  0.004   0.043   2682
  Dihedral  :  4.082  19.934   2063
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.13 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.94 (0.20), residues: 1910
  helix:  1.27 (0.19), residues: 813
  sheet: -1.32 (0.32), residues: 256
  loop : -2.40 (0.21), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 283 
 HIS   0.006   0.001   HIS C 157 
 PHE   0.010   0.001   PHE B 509 
 TYR   0.024   0.001   TYR C 107 
 ARG   0.006   0.000   ARG C  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (  438)
  hydrogen bonds       : angle       3.31235 ( 1314)
  metal coordination   : bond        0.00263 (    3)
  covalent geometry    : bond        0.00226 (15411)
  covalent geometry    : angle       0.52571 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 1.614 
Fit side-chains
REVERT: A  373 GLU cc_start: 0.7694 (tt0) cc_final: 0.7161 (tm-30)
REVERT: A  454 LEU cc_start: 0.9103 (tp) cc_final: 0.8693 (tt)
REVERT: B   27 ASP cc_start: 0.7214 (m-30) cc_final: 0.6917 (m-30)
REVERT: B  486 MET cc_start: 0.7631 (mtm) cc_final: 0.6672 (tpt)
REVERT: C  208 THR cc_start: 0.8516 (p) cc_final: 0.8135 (p)
REVERT: C  259 MET cc_start: 0.8051 (mmm) cc_final: 0.7840 (mmm)
REVERT: C  273 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4972 (mp0)
REVERT: C  278 TYR cc_start: 0.5544 (p90) cc_final: 0.4774 (p90)
REVERT: C  310 ARG cc_start: 0.6714 (ttp80) cc_final: 0.6470 (ttp80)
REVERT: D  241 ILE cc_start: 0.7341 (mp) cc_final: 0.6987 (mp)
REVERT: D  362 ASN cc_start: 0.8315 (p0) cc_final: 0.7885 (p0)
REVERT: D  363 ASP cc_start: 0.6267 (t0) cc_final: 0.5730 (t0)
  outliers start: 31
  outliers final: 24
  residues processed: 191
  average time/residue: 0.2527
  time to fit residues: 74.0362
Evaluate side-chains
  178 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 1.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  302 PHE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  344 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 117 optimal weight:    6.9990
   chunk 136 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0370
   chunk 39 optimal weight:    0.6980
   chunk 143 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 184 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.137964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.109685 restraints weight = 25094.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.109086 restraints weight = 33659.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111080 restraints weight = 26746.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15414  Z= 0.106
  Angle     :  0.545   7.856  20961  Z= 0.269
  Chirality :  0.041   0.142   2416
  Planarity :  0.004   0.041   2682
  Dihedral  :  4.003  19.821   2063
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.95 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.83 (0.20), residues: 1910
  helix:  1.33 (0.19), residues: 813
  sheet: -1.30 (0.32), residues: 270
  loop : -2.30 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 283 
 HIS   0.007   0.001   HIS C 157 
 PHE   0.010   0.001   PHE B 509 
 TYR   0.027   0.001   TYR C 107 
 ARG   0.009   0.000   ARG C 231 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02846 (  438)
  hydrogen bonds       : angle       3.33367 ( 1314)
  metal coordination   : bond        0.00196 (    3)
  covalent geometry    : bond        0.00248 (15411)
  covalent geometry    : angle       0.54478 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 158
  time to evaluate  : 1.571 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7694 (mp10) cc_final: 0.7470 (mm-40)
REVERT: A  373 GLU cc_start: 0.7895 (tt0) cc_final: 0.7272 (tm-30)
REVERT: A  454 LEU cc_start: 0.9142 (tp) cc_final: 0.8732 (tt)
REVERT: B   27 ASP cc_start: 0.7223 (m-30) cc_final: 0.6916 (m-30)
REVERT: B   93 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5762 (tt)
REVERT: B  486 MET cc_start: 0.7518 (mtm) cc_final: 0.6987 (tpt)
REVERT: C   56 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7740 (ptt90)
REVERT: C  208 THR cc_start: 0.8689 (p) cc_final: 0.8352 (p)
REVERT: C  259 MET cc_start: 0.8020 (mmm) cc_final: 0.7808 (mmm)
REVERT: C  273 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4915 (mp0)
REVERT: C  278 TYR cc_start: 0.5536 (p90) cc_final: 0.4830 (p90)
REVERT: D  207 GLN cc_start: 0.6767 (tm130) cc_final: 0.6530 (tm-30)
REVERT: D  241 ILE cc_start: 0.7337 (mp) cc_final: 0.7006 (mp)
REVERT: D  291 LEU cc_start: 0.6628 (pt) cc_final: 0.6384 (tt)
REVERT: D  362 ASN cc_start: 0.8308 (p0) cc_final: 0.7878 (p0)
REVERT: D  363 ASP cc_start: 0.6256 (t0) cc_final: 0.5698 (t0)
  outliers start: 37
  outliers final: 33
  residues processed: 186
  average time/residue: 0.2466
  time to fit residues: 70.4433
Evaluate side-chains
  188 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 1.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  302 PHE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 158 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 138 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 149 optimal weight:    0.0670
   chunk 115 optimal weight:    7.9990
   overall best weight:    0.8722

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.137901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110280 restraints weight = 25014.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109713 restraints weight = 35952.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111000 restraints weight = 30374.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15414  Z= 0.115
  Angle     :  0.550   8.063  20961  Z= 0.271
  Chirality :  0.041   0.155   2416
  Planarity :  0.004   0.044   2682
  Dihedral  :  3.995  19.386   2063
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.13 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.74 (0.20), residues: 1910
  helix:  1.38 (0.19), residues: 809
  sheet: -1.26 (0.32), residues: 270
  loop : -2.21 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP D 283 
 HIS   0.007   0.001   HIS C 157 
 PHE   0.011   0.001   PHE B 509 
 TYR   0.028   0.001   TYR C 107 
 ARG   0.006   0.000   ARG C 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02964 (  438)
  hydrogen bonds       : angle       3.37195 ( 1314)
  metal coordination   : bond        0.00281 (    3)
  covalent geometry    : bond        0.00273 (15411)
  covalent geometry    : angle       0.55032 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 155
  time to evaluate  : 1.715 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7657 (mp10) cc_final: 0.7386 (mm-40)
REVERT: A  373 GLU cc_start: 0.7894 (tt0) cc_final: 0.7312 (tm-30)
REVERT: A  454 LEU cc_start: 0.9167 (tp) cc_final: 0.8783 (tt)
REVERT: A  591 SER cc_start: 0.8321 (t) cc_final: 0.7851 (p)
REVERT: B   27 ASP cc_start: 0.7233 (m-30) cc_final: 0.6944 (m-30)
REVERT: B   93 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5820 (tt)
REVERT: C  208 THR cc_start: 0.8656 (p) cc_final: 0.8333 (p)
REVERT: C  273 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.5045 (mp0)
REVERT: C  278 TYR cc_start: 0.5552 (p90) cc_final: 0.4922 (p90)
REVERT: D  241 ILE cc_start: 0.7259 (mp) cc_final: 0.6935 (mp)
REVERT: D  362 ASN cc_start: 0.8273 (p0) cc_final: 0.7873 (p0)
REVERT: D  363 ASP cc_start: 0.6259 (t0) cc_final: 0.5649 (t0)
  outliers start: 38
  outliers final: 35
  residues processed: 185
  average time/residue: 0.2682
  time to fit residues: 78.2260
Evaluate side-chains
  188 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  302 PHE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 146 optimal weight:    0.2980
   chunk 183 optimal weight:    9.9990
   chunk 100 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 123 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 141 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 167 optimal weight:    7.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.138942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109935 restraints weight = 25138.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.108596 restraints weight = 32903.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.109580 restraints weight = 34911.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  15414  Z= 0.096
  Angle     :  0.546  12.571  20961  Z= 0.266
  Chirality :  0.040   0.152   2416
  Planarity :  0.004   0.042   2682
  Dihedral  :  3.887  18.914   2063
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.37 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.63 (0.20), residues: 1910
  helix:  1.51 (0.19), residues: 808
  sheet: -1.31 (0.31), residues: 284
  loop : -2.14 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 283 
 HIS   0.007   0.001   HIS C 157 
 PHE   0.009   0.001   PHE B 509 
 TYR   0.026   0.001   TYR C 107 
 ARG   0.007   0.000   ARG C 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02710 (  438)
  hydrogen bonds       : angle       3.27009 ( 1314)
  metal coordination   : bond        0.00326 (    3)
  covalent geometry    : bond        0.00223 (15411)
  covalent geometry    : angle       0.54649 (20961)

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

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

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3820 Ramachandran restraints generated.
    1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 1.745 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7630 (mp10) cc_final: 0.7410 (mm-40)
REVERT: A  373 GLU cc_start: 0.7806 (tt0) cc_final: 0.7252 (tm-30)
REVERT: A  591 SER cc_start: 0.8279 (t) cc_final: 0.7893 (p)
REVERT: B   27 ASP cc_start: 0.7254 (m-30) cc_final: 0.6932 (m-30)
REVERT: B   93 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5736 (tt)
REVERT: C  208 THR cc_start: 0.8571 (p) cc_final: 0.8254 (p)
REVERT: C  273 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.4996 (mp0)
REVERT: C  278 TYR cc_start: 0.5502 (p90) cc_final: 0.4847 (p90)
REVERT: C  327 MET cc_start: 0.7292 (ptp) cc_final: 0.7008 (ptp)
REVERT: C  437 MET cc_start: 0.7458 (ttt) cc_final: 0.7224 (ttt)
REVERT: D  241 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6735 (mp)
REVERT: D  362 ASN cc_start: 0.8292 (p0) cc_final: 0.7869 (p0)
REVERT: D  363 ASP cc_start: 0.6292 (t0) cc_final: 0.5747 (t0)
  outliers start: 36
  outliers final: 31
  residues processed: 188
  average time/residue: 0.2475
  time to fit residues: 71.4756
Evaluate side-chains
  189 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  273 GLU
Chi-restraints excluded: chain C residue  302 PHE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  344 VAL
Chi-restraints excluded: chain D residue  368 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 118 optimal weight:    0.3980
   chunk 75 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.138631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111127 restraints weight = 25159.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.110869 restraints weight = 35510.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.111877 restraints weight = 36572.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15414  Z= 0.105
  Angle     :  0.564  12.315  20961  Z= 0.274
  Chirality :  0.041   0.183   2416
  Planarity :  0.004   0.040   2682
  Dihedral  :  3.862  19.190   2063
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.49 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.58 (0.20), residues: 1910
  helix:  1.52 (0.19), residues: 809
  sheet: -1.22 (0.32), residues: 283
  loop : -2.10 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP D 283 
 HIS   0.007   0.001   HIS C 157 
 PHE   0.012   0.001   PHE A 701 
 TYR   0.026   0.001   TYR C 107 
 ARG   0.007   0.000   ARG C 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  438)
  hydrogen bonds       : angle       3.28979 ( 1314)
  metal coordination   : bond        0.00251 (    3)
  covalent geometry    : bond        0.00247 (15411)
  covalent geometry    : angle       0.56411 (20961)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4267.22 seconds
wall clock time: 76 minutes 21.18 seconds (4581.18 seconds total)