Starting phenix.real_space_refine
on Sat Aug 23 00:42:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bw7_30229/08_2025/7bw7_30229.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5621      2.51       5
     N    1509      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8824
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5224
          Classifications: {'peptide': 647}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 613}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3224
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 19, 'TRANS': 376}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 376
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
          Chain breaks: 1
  Time building chain proxies: 1.52, per 1000 atoms: 0.17
  Number of scatterers: 8824
  At special positions: 0
  Unit cell: (91.79, 108.23, 153.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1638      8.00
     N    1509      7.00
     C    5621      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 786 " - pdb=" SG  CYS A 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 786 " - pdb=" SG  CYS C 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  75 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  66 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 328.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      13.2% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 20
      removed outlier: 3.745A  pdb=" N   ARG A  19 " --> pdb=" O   ASN A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.558A  pdb=" N   ASP A 142 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 200
      removed outlier: 3.956A  pdb=" N   HIS A 199 " --> pdb=" O   CYS A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.854A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   CYS A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ASN A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.751A  pdb=" N   GLY A 317 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 318 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 314 through 318'
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 350 through 358
      removed outlier: 3.515A  pdb=" N   LEU A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.777A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 638 through 642
    Processing helix  chain 'C' and resid 314 through 316
      No H-bonds generated for 'chain 'C' and resid 314 through 316'
    Processing helix  chain 'C' and resid 323 through 328
    Processing helix  chain 'C' and resid 329 through 331
      No H-bonds generated for 'chain 'C' and resid 329 through 331'
    Processing helix  chain 'C' and resid 352 through 357
    Processing helix  chain 'C' and resid 435 through 440
      removed outlier: 4.208A  pdb=" N   ILE C 439 " --> pdb=" O   CYS C 435 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   HIS C 440 " --> pdb=" O   LEU C 436 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 435 through 440'
    Processing helix  chain 'C' and resid 440 through 445
    Processing helix  chain 'C' and resid 496 through 500
    Processing helix  chain 'C' and resid 692 through 710
      removed outlier: 3.730A  pdb=" N   GLU C 698 " --> pdb=" O   LYS C 694 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   SER C 700 " --> pdb=" O   LEU C 696 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LYS C 703 " --> pdb=" O   SER C 699 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 19
      removed outlier: 3.824A  pdb=" N   CYS D  19 " --> pdb=" O   LEU D  15 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 6.586A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57
      removed outlier: 3.517A  pdb=" N   ILE A  82 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.816A  pdb=" N   ASN A 148 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248
      removed outlier: 3.736A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE A 248 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280
    Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312
      removed outlier: 3.521A  pdb=" N   CYS A 312 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 480
      removed outlier: 6.560A  pdb=" N   ARG A 488 " --> pdb=" O   SER A 476 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE A 478 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LEU A 486 " --> pdb=" O   ILE A 478 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 533
      removed outlier: 3.948A  pdb=" N   THR A 530 " --> pdb=" O   TYR A 507 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   TYR A 507 " --> pdb=" O   THR A 530 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   VAL A 566 " --> pdb=" O   ASP A 584 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ASP A 584 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 602
      removed outlier: 6.607A  pdb=" N   LYS A 614 " --> pdb=" O   PRO A 601 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 321
      removed outlier: 6.590A  pdb=" N   LYS C 319 " --> pdb=" O   ILE C 341 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU C 340 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 531 through 533
      removed outlier: 3.542A  pdb=" N   VAL C 532 " --> pdb=" O   LEU C 505 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 599 through 605
      removed outlier: 4.858A  pdb=" N   ASP C 600 " --> pdb=" O   LYS C 616 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 631
      removed outlier: 3.651A  pdb=" N   GLU C 782 " --> pdb=" O   PHE C 631 " (cutoff:3.500A)

    119 hydrogen bonds defined for protein.
    279 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: 1.01

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2764
        1.34 -     1.46: 2073
        1.46 -     1.58: 4125
        1.58 -     1.71: 0
        1.71 -     1.83: 70
  Bond restraints: 9032
  Sorted by residual:
  bond pdb=" C   VAL C 597 "
       pdb=" N   PRO C 598 "
    ideal  model  delta    sigma   weight residual
    1.330  1.377 -0.047 1.25e-02 6.40e+03 1.41e+01
  bond pdb=" CA  LEU C 696 "
       pdb=" C   LEU C 696 "
    ideal  model  delta    sigma   weight residual
    1.522  1.457  0.064 1.72e-02 3.38e+03 1.39e+01
  bond pdb=" N   VAL A 377 "
       pdb=" CA  VAL A 377 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.08e-02 8.57e+03 1.24e+01
  bond pdb=" N   GLY C 580 "
       pdb=" CA  GLY C 580 "
    ideal  model  delta    sigma   weight residual
    1.446  1.485 -0.039 1.13e-02 7.83e+03 1.19e+01
  bond pdb=" N   THR C 578 "
       pdb=" CA  THR C 578 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 1.02e+01
  ... (remaining 9027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 11418
        1.95 -     3.90: 687
        3.90 -     5.86: 101
        5.86 -     7.81: 18
        7.81 -     9.76: 9
  Bond angle restraints: 12233
  Sorted by residual:
  angle pdb=" C   TYR C 579 "
        pdb=" CA  TYR C 579 "
        pdb=" CB  TYR C 579 "
      ideal   model   delta    sigma   weight residual
     110.04  100.28    9.76 1.51e+00 4.39e-01 4.18e+01
  angle pdb=" N   PRO C 621 "
        pdb=" CA  PRO C 621 "
        pdb=" C   PRO C 621 "
      ideal   model   delta    sigma   weight residual
     113.86  106.93    6.93 1.25e+00 6.40e-01 3.07e+01
  angle pdb=" N   PRO A 432 "
        pdb=" CA  PRO A 432 "
        pdb=" C   PRO A 432 "
      ideal   model   delta    sigma   weight residual
     113.40  120.78   -7.38 1.34e+00 5.57e-01 3.04e+01
  angle pdb=" C   VAL C 597 "
        pdb=" N   PRO C 598 "
        pdb=" CA  PRO C 598 "
      ideal   model   delta    sigma   weight residual
     120.21  125.30   -5.09 9.60e-01 1.09e+00 2.81e+01
  angle pdb=" N   VAL A 324 "
        pdb=" CA  VAL A 324 "
        pdb=" C   VAL A 324 "
      ideal   model   delta    sigma   weight residual
     111.89  104.50    7.39 1.44e+00 4.82e-01 2.64e+01
  ... (remaining 12228 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4697
       17.95 -    35.90: 610
       35.90 -    53.85: 129
       53.85 -    71.80: 14
       71.80 -    89.75: 9
  Dihedral angle restraints: 5459
    sinusoidal: 2267
      harmonic: 3192
  Sorted by residual:
  dihedral pdb=" CB  CYS D  19 "
           pdb=" SG  CYS D  19 "
           pdb=" SG  CYS D  75 "
           pdb=" CB  CYS D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.20   65.20     1      1.00e+01 1.00e-02 5.57e+01
  dihedral pdb=" CB  CYS A 228 "
           pdb=" SG  CYS A 228 "
           pdb=" SG  CYS A 237 "
           pdb=" CB  CYS A 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.19   59.19     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CA  CYS A 207 "
           pdb=" C   CYS A 207 "
           pdb=" N   CYS A 208 "
           pdb=" CA  CYS A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 5456 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1020
       0.067 -    0.133: 274
       0.133 -    0.200: 39
       0.200 -    0.266: 3
       0.266 -    0.333: 1
  Chirality restraints: 1337
  Sorted by residual:
  chirality pdb=" CA  PRO A 432 "
            pdb=" N   PRO A 432 "
            pdb=" C   PRO A 432 "
            pdb=" CB  PRO A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CG  LEU C 434 "
            pdb=" CB  LEU C 434 "
            pdb=" CD1 LEU C 434 "
            pdb=" CD2 LEU C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ILE C 457 "
            pdb=" N   ILE C 457 "
            pdb=" C   ILE C 457 "
            pdb=" CB  ILE C 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1334 not shown)

  Planarity restraints: 1568
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 577 "   -0.022 2.00e-02 2.50e+03   4.53e-02 2.05e+01
        pdb=" C   ARG C 577 "    0.078 2.00e-02 2.50e+03
        pdb=" O   ARG C 577 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   THR C 578 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 494 "   -0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO C 495 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO C 495 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 495 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 591 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.92e+00
        pdb=" C   ASP C 591 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ASP C 591 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA C 592 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1565 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 245
        2.62 -     3.19: 8823
        3.19 -     3.76: 13629
        3.76 -     4.33: 18090
        4.33 -     4.90: 27791
  Nonbonded interactions: 68578
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 437 "
            pdb=" O   GLU C 517 "
     model   vdw
     2.050 3.040
  nonbonded pdb=" OG  SER A 116 "
            pdb=" OD1 ASN A 143 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG  SER A 198 "
            pdb=" NE  ARG A 229 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OH  TYR A 628 "
            pdb=" OE2 GLU A 766 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" OG  SER D  67 "
            pdb=" OE1 GLN D  70 "
     model   vdw
     2.141 3.040
  ... (remaining 68573 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=1.00 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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.850
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
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      :  0.008   0.078   9049  Z= 0.396
  Angle     :  1.062   9.759  12267  Z= 0.608
  Chirality :  0.060   0.333   1337
  Planarity :  0.006   0.066   1568
  Dihedral  : 16.200  89.747   3340
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 40.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.38 %
    Favored  : 76.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.62 (0.21), residues: 1065
  helix: -3.74 (0.35), residues: 101
  sheet: -3.83 (0.34), residues: 190
  loop : -4.03 (0.19), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 118 
 TYR   0.027   0.003   TYR D  26 
 PHE   0.029   0.003   PHE A 400 
 TRP   0.022   0.003   TRP A 183 
 HIS   0.007   0.002   HIS D   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00771 ( 9032)
  covalent geometry    : angle       1.05605 (12233)
  SS BOND              : bond        0.00511 (   17)
  SS BOND              : angle       2.36126 (   34)
  hydrogen bonds       : bond        0.20597 (  119)
  hydrogen bonds       : angle      11.12800 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.7987 (tt) cc_final: 0.7682 (tp)
REVERT: A  246 TYR cc_start: 0.7658 (m-80) cc_final: 0.7110 (m-80)
REVERT: A  382 PHE cc_start: 0.8574 (m-10) cc_final: 0.8320 (m-10)
REVERT: A  513 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6743 (mp10)
REVERT: A  616 LYS cc_start: 0.9016 (tppt) cc_final: 0.8632 (tppt)
REVERT: A  780 ARG cc_start: 0.7569 (ptt180) cc_final: 0.7125 (ptm-80)
REVERT: C  355 GLU cc_start: 0.7858 (tt0) cc_final: 0.7392 (pt0)
REVERT: C  382 PHE cc_start: 0.8463 (t80) cc_final: 0.7999 (t80)
REVERT: C  552 LEU cc_start: 0.9076 (tp) cc_final: 0.8812 (tp)
REVERT: C  780 ARG cc_start: 0.7148 (ttt-90) cc_final: 0.6133 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1146
  time to fit residues: 23.3996
Evaluate side-chains
  117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  90 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 610 GLN
** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.183171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.145160 restraints weight = 19295.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.145815 restraints weight = 15019.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.147435 restraints weight = 12219.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.147860 restraints weight = 10515.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.148125 restraints weight = 10610.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6646
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9049  Z= 0.192
  Angle     :  0.856  11.357  12267  Z= 0.437
  Chirality :  0.052   0.178   1337
  Planarity :  0.005   0.056   1568
  Dihedral  :  7.682  27.052   1184
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 21.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.31 %
    Favored  : 81.69 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 13.02 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.30 (0.22), residues: 1065
  helix: -3.32 (0.36), residues: 108
  sheet: -3.84 (0.33), residues: 196
  loop : -3.74 (0.19), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  22 
 TYR   0.024   0.002   TYR A 430 
 PHE   0.016   0.002   PHE A 381 
 TRP   0.031   0.002   TRP C 632 
 HIS   0.007   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 9032)
  covalent geometry    : angle       0.85307 (12233)
  SS BOND              : bond        0.00334 (   17)
  SS BOND              : angle       1.60935 (   34)
  hydrogen bonds       : bond        0.05429 (  119)
  hydrogen bonds       : angle       9.28555 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6860 (mmm160) cc_final: 0.6342 (mmt180)
REVERT: A  246 TYR cc_start: 0.7023 (m-80) cc_final: 0.6536 (m-80)
REVERT: A  294 MET cc_start: 0.6108 (ppp) cc_final: 0.5850 (ppp)
REVERT: A  355 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8221 (pp20)
REVERT: A  425 LYS cc_start: 0.7219 (ttmt) cc_final: 0.6852 (tmtt)
REVERT: A  426 LEU cc_start: 0.7500 (tt) cc_final: 0.6847 (tt)
REVERT: A  472 LEU cc_start: 0.6830 (tp) cc_final: 0.6550 (pt)
REVERT: A  513 GLN cc_start: 0.7438 (tp-100) cc_final: 0.6724 (mp10)
REVERT: A  616 LYS cc_start: 0.8791 (tppt) cc_final: 0.8363 (tppt)
REVERT: C  355 GLU cc_start: 0.7729 (tt0) cc_final: 0.7264 (pt0)
REVERT: C  381 PHE cc_start: 0.8583 (p90) cc_final: 0.8061 (p90)
REVERT: C  382 PHE cc_start: 0.8250 (t80) cc_final: 0.7857 (t80)
REVERT: C  409 ARG cc_start: 0.6200 (mtt90) cc_final: 0.5965 (mmt90)
REVERT: C  552 LEU cc_start: 0.9116 (tp) cc_final: 0.7995 (tp)
REVERT: C  780 ARG cc_start: 0.6833 (ttt-90) cc_final: 0.5754 (mtp85)
  outliers start: 2
  outliers final: 1
  residues processed: 159
  average time/residue: 0.0947
  time to fit residues: 20.1338
Evaluate side-chains
  118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0270
   chunk 38 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0040
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.2056

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 ASN
A 594 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 711 ASN
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.227330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.197761 restraints weight = 21972.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.194859 restraints weight = 24840.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.193596 restraints weight = 21037.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.193888 restraints weight = 19792.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.193633 restraints weight = 17097.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9049  Z= 0.158
  Angle     :  0.799  10.902  12267  Z= 0.411
  Chirality :  0.051   0.170   1337
  Planarity :  0.005   0.049   1568
  Dihedral  :  7.202  29.437   1184
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.49 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.85 (0.22), residues: 1065
  helix: -2.95 (0.40), residues: 108
  sheet: -3.62 (0.35), residues: 175
  loop : -3.44 (0.19), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 774 
 TYR   0.030   0.002   TYR C 430 
 PHE   0.016   0.002   PHE A 382 
 TRP   0.023   0.002   TRP A 251 
 HIS   0.007   0.001   HIS C 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9032)
  covalent geometry    : angle       0.79507 (12233)
  SS BOND              : bond        0.00471 (   17)
  SS BOND              : angle       1.70553 (   34)
  hydrogen bonds       : bond        0.04812 (  119)
  hydrogen bonds       : angle       8.55866 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6757 (mmm160) cc_final: 0.5998 (mmt180)
REVERT: A  294 MET cc_start: 0.5896 (ppp) cc_final: 0.5648 (ppp)
REVERT: A  430 TYR cc_start: 0.7841 (m-10) cc_final: 0.7573 (m-80)
REVERT: A  513 GLN cc_start: 0.7424 (tp-100) cc_final: 0.6762 (mp10)
REVERT: A  616 LYS cc_start: 0.8694 (tppt) cc_final: 0.8223 (tppt)
REVERT: A  765 LYS cc_start: 0.7972 (mttp) cc_final: 0.7181 (mttm)
REVERT: A  783 LEU cc_start: 0.9075 (tp) cc_final: 0.8381 (tp)
REVERT: C  355 GLU cc_start: 0.7397 (tt0) cc_final: 0.7098 (pt0)
REVERT: C  370 ILE cc_start: 0.8213 (mm) cc_final: 0.7983 (mm)
REVERT: C  381 PHE cc_start: 0.8221 (p90) cc_final: 0.7973 (p90)
REVERT: C  382 PHE cc_start: 0.8217 (t80) cc_final: 0.7838 (t80)
REVERT: C  552 LEU cc_start: 0.9004 (tp) cc_final: 0.8735 (tp)
REVERT: C  780 ARG cc_start: 0.6721 (ttt-90) cc_final: 0.5649 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0871
  time to fit residues: 19.4994
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 85 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 16 optimal weight:    0.0040
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
A 406 GLN
A 429 HIS
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.192340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.160765 restraints weight = 19356.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.164330 restraints weight = 18719.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.165470 restraints weight = 15112.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.166929 restraints weight = 10585.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.168303 restraints weight = 9293.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6239
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9049  Z= 0.138
  Angle     :  0.739  10.250  12267  Z= 0.380
  Chirality :  0.049   0.162   1337
  Planarity :  0.005   0.049   1568
  Dihedral  :  6.734  29.071   1184
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.71 %
    Favored  : 86.29 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.44 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.53 (0.23), residues: 1065
  helix: -2.65 (0.43), residues: 112
  sheet: -3.39 (0.34), residues: 180
  loop : -3.21 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 539 
 TYR   0.023   0.002   TYR A  60 
 PHE   0.019   0.002   PHE A 381 
 TRP   0.018   0.002   TRP C 412 
 HIS   0.006   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9032)
  covalent geometry    : angle       0.73495 (12233)
  SS BOND              : bond        0.00328 (   17)
  SS BOND              : angle       1.56984 (   34)
  hydrogen bonds       : bond        0.04195 (  119)
  hydrogen bonds       : angle       8.00240 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6595 (mmm160) cc_final: 0.5901 (mmt180)
REVERT: A  294 MET cc_start: 0.5770 (ppp) cc_final: 0.5504 (ppp)
REVERT: A  360 LEU cc_start: 0.7596 (mm) cc_final: 0.6888 (tt)
REVERT: A  406 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8209 (mm-40)
REVERT: A  425 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7314 (tmtt)
REVERT: A  513 GLN cc_start: 0.7359 (tp-100) cc_final: 0.6576 (mp10)
REVERT: A  616 LYS cc_start: 0.8807 (tttp) cc_final: 0.8511 (tppt)
REVERT: A  765 LYS cc_start: 0.7739 (mttp) cc_final: 0.6936 (mttm)
REVERT: A  783 LEU cc_start: 0.8615 (tp) cc_final: 0.8319 (tp)
REVERT: C  552 LEU cc_start: 0.9012 (tp) cc_final: 0.8720 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.0879
  time to fit residues: 18.2765
Evaluate side-chains
  122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
A 337 ASN
A 410 GLN
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 470 ASN
C 561 GLN
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.182494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.138650 restraints weight = 19493.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.141396 restraints weight = 14581.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.143180 restraints weight = 12036.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144461 restraints weight = 10599.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.144891 restraints weight = 9742.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   9049  Z= 0.262
  Angle     :  0.853   9.760  12267  Z= 0.439
  Chirality :  0.051   0.186   1337
  Planarity :  0.005   0.050   1568
  Dihedral  :  7.297  30.000   1184
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 23.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.22 %
    Favored  : 81.78 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.45 %
    Favored  : 94.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.69 (0.23), residues: 1065
  helix: -2.78 (0.41), residues: 116
  sheet: -3.35 (0.34), residues: 201
  loop : -3.34 (0.20), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 539 
 TYR   0.033   0.003   TYR A 401 
 PHE   0.026   0.003   PHE C 714 
 TRP   0.017   0.002   TRP C 551 
 HIS   0.009   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 9032)
  covalent geometry    : angle       0.84964 (12233)
  SS BOND              : bond        0.00428 (   17)
  SS BOND              : angle       1.71569 (   34)
  hydrogen bonds       : bond        0.04748 (  119)
  hydrogen bonds       : angle       8.72012 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6127 (mmt180)
REVERT: A  110 MET cc_start: 0.7871 (mmm) cc_final: 0.7622 (mmm)
REVERT: A  425 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6788 (tmtt)
REVERT: A  513 GLN cc_start: 0.7266 (tp-100) cc_final: 0.6609 (mp10)
REVERT: A  562 TYR cc_start: 0.7693 (m-10) cc_final: 0.7403 (m-10)
REVERT: A  616 LYS cc_start: 0.8967 (tttp) cc_final: 0.8668 (tppt)
REVERT: A  765 LYS cc_start: 0.7784 (mttp) cc_final: 0.7014 (mttm)
REVERT: C  430 TYR cc_start: 0.6596 (t80) cc_final: 0.6106 (t80)
REVERT: C  518 PHE cc_start: 0.7795 (t80) cc_final: 0.7590 (t80)
REVERT: C  552 LEU cc_start: 0.9231 (tp) cc_final: 0.8886 (tp)
REVERT: C  780 ARG cc_start: 0.6517 (ttt-90) cc_final: 0.5578 (mtp85)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0831
  time to fit residues: 15.9719
Evaluate side-chains
  103 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 98 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 622 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.186821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.155320 restraints weight = 19216.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.161692 restraints weight = 22438.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.162943 restraints weight = 13420.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.164034 restraints weight = 10499.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.164578 restraints weight = 9422.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9049  Z= 0.157
  Angle     :  0.778  11.222  12267  Z= 0.397
  Chirality :  0.050   0.215   1337
  Planarity :  0.005   0.047   1568
  Dihedral  :  6.824  28.329   1184
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.08 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.48 (0.23), residues: 1065
  helix: -2.71 (0.43), residues: 112
  sheet: -3.18 (0.36), residues: 176
  loop : -3.21 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 539 
 TYR   0.023   0.002   TYR D  74 
 PHE   0.041   0.002   PHE C 475 
 TRP   0.017   0.002   TRP C 412 
 HIS   0.013   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9032)
  covalent geometry    : angle       0.77492 (12233)
  SS BOND              : bond        0.00331 (   17)
  SS BOND              : angle       1.59257 (   34)
  hydrogen bonds       : bond        0.04039 (  119)
  hydrogen bonds       : angle       8.10663 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6655 (mmm160) cc_final: 0.5859 (mmt180)
REVERT: A  110 MET cc_start: 0.7805 (mmm) cc_final: 0.7584 (mmm)
REVERT: A  360 LEU cc_start: 0.7609 (mm) cc_final: 0.6992 (tt)
REVERT: A  404 ASP cc_start: 0.8253 (t0) cc_final: 0.8044 (t0)
REVERT: A  513 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6626 (mp10)
REVERT: A  616 LYS cc_start: 0.8697 (tttp) cc_final: 0.8444 (tppt)
REVERT: A  765 LYS cc_start: 0.7405 (mttp) cc_final: 0.6759 (mttm)
REVERT: A  783 LEU cc_start: 0.8569 (tp) cc_final: 0.8304 (tp)
REVERT: C  475 PHE cc_start: 0.7983 (m-80) cc_final: 0.7622 (m-80)
REVERT: C  552 LEU cc_start: 0.9214 (tp) cc_final: 0.8934 (tp)
REVERT: C  695 GLU cc_start: 0.7216 (pm20) cc_final: 0.6980 (pm20)
REVERT: C  780 ARG cc_start: 0.6594 (ttt-90) cc_final: 0.5686 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1070
  time to fit residues: 21.3585
Evaluate side-chains
  118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 77 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.184557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.141849 restraints weight = 19294.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144847 restraints weight = 14045.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.146848 restraints weight = 11388.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.148020 restraints weight = 9880.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.149030 restraints weight = 9068.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9049  Z= 0.196
  Angle     :  0.792  11.420  12267  Z= 0.404
  Chirality :  0.049   0.171   1337
  Planarity :  0.005   0.047   1568
  Dihedral  :  6.930  28.939   1184
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 19.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.65 %
    Favored  : 82.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.44 (0.23), residues: 1065
  helix: -2.78 (0.43), residues: 112
  sheet: -3.06 (0.35), residues: 188
  loop : -3.18 (0.21), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 539 
 TYR   0.024   0.002   TYR A 401 
 PHE   0.030   0.002   PHE C 475 
 TRP   0.012   0.002   TRP C 489 
 HIS   0.017   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 9032)
  covalent geometry    : angle       0.78810 (12233)
  SS BOND              : bond        0.00290 (   17)
  SS BOND              : angle       1.63252 (   34)
  hydrogen bonds       : bond        0.04087 (  119)
  hydrogen bonds       : angle       8.24331 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6760 (mmm160) cc_final: 0.6058 (mmt180)
REVERT: A  110 MET cc_start: 0.7846 (mmm) cc_final: 0.7562 (mmm)
REVERT: A  360 LEU cc_start: 0.7719 (mm) cc_final: 0.7012 (tt)
REVERT: A  404 ASP cc_start: 0.8677 (t0) cc_final: 0.8465 (t0)
REVERT: A  425 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6763 (tmtt)
REVERT: A  513 GLN cc_start: 0.7258 (tp-100) cc_final: 0.6647 (mp10)
REVERT: A  562 TYR cc_start: 0.7050 (m-80) cc_final: 0.6747 (m-10)
REVERT: A  616 LYS cc_start: 0.8881 (tttp) cc_final: 0.8584 (tppt)
REVERT: A  765 LYS cc_start: 0.7754 (mttp) cc_final: 0.7013 (mttm)
REVERT: C  518 PHE cc_start: 0.7419 (t80) cc_final: 0.7094 (t80)
REVERT: C  552 LEU cc_start: 0.9300 (tp) cc_final: 0.9010 (tp)
REVERT: C  780 ARG cc_start: 0.6367 (ttt-90) cc_final: 0.5372 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1108
  time to fit residues: 20.6026
Evaluate side-chains
  106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 101 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.187466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144965 restraints weight = 19134.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.148139 restraints weight = 13947.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.150419 restraints weight = 11184.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.151989 restraints weight = 9567.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.153043 restraints weight = 8640.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9049  Z= 0.156
  Angle     :  0.759  11.390  12267  Z= 0.384
  Chirality :  0.049   0.184   1337
  Planarity :  0.005   0.066   1568
  Dihedral  :  6.647  28.057   1184
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.05 %
    Favored  : 86.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.24 (0.23), residues: 1065
  helix: -2.74 (0.43), residues: 111
  sheet: -2.88 (0.38), residues: 169
  loop : -3.05 (0.20), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 236 
 TYR   0.029   0.002   TYR A 374 
 PHE   0.028   0.002   PHE C 475 
 TRP   0.013   0.002   TRP C 489 
 HIS   0.015   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9032)
  covalent geometry    : angle       0.75592 (12233)
  SS BOND              : bond        0.00390 (   17)
  SS BOND              : angle       1.43161 (   34)
  hydrogen bonds       : bond        0.03730 (  119)
  hydrogen bonds       : angle       7.88888 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6704 (mmm160) cc_final: 0.6026 (mmt180)
REVERT: A  110 MET cc_start: 0.7785 (mmm) cc_final: 0.7548 (mmm)
REVERT: A  329 GLU cc_start: 0.7790 (mp0) cc_final: 0.7257 (mm-30)
REVERT: A  360 LEU cc_start: 0.7715 (mm) cc_final: 0.7048 (tt)
REVERT: A  404 ASP cc_start: 0.8708 (t0) cc_final: 0.8360 (t0)
REVERT: A  513 GLN cc_start: 0.7389 (tp-100) cc_final: 0.6656 (mp10)
REVERT: A  562 TYR cc_start: 0.7044 (m-80) cc_final: 0.6734 (m-10)
REVERT: A  616 LYS cc_start: 0.8873 (tttp) cc_final: 0.8562 (tppt)
REVERT: A  765 LYS cc_start: 0.7674 (mttp) cc_final: 0.6941 (mttm)
REVERT: C  382 PHE cc_start: 0.8413 (t80) cc_final: 0.7998 (t80)
REVERT: C  518 PHE cc_start: 0.7322 (t80) cc_final: 0.7087 (t80)
REVERT: C  552 LEU cc_start: 0.9254 (tp) cc_final: 0.9030 (tp)
REVERT: C  780 ARG cc_start: 0.6304 (ttt-90) cc_final: 0.5369 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1117
  time to fit residues: 22.1289
Evaluate side-chains
  118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0970
   chunk 36 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
A 452 GLN
C 622 ASN
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.193614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.150472 restraints weight = 18998.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.154324 restraints weight = 12974.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.156944 restraints weight = 10114.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.158839 restraints weight = 8523.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.159709 restraints weight = 7589.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9049  Z= 0.128
  Angle     :  0.727  11.763  12267  Z= 0.365
  Chirality :  0.048   0.198   1337
  Planarity :  0.005   0.054   1568
  Dihedral  :  6.310  26.675   1184
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.68 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.02 (0.23), residues: 1065
  helix: -2.69 (0.41), residues: 117
  sheet: -2.60 (0.39), residues: 168
  loop : -2.90 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 236 
 TYR   0.024   0.002   TYR D  74 
 PHE   0.027   0.002   PHE C 475 
 TRP   0.022   0.002   TRP C 412 
 HIS   0.010   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9032)
  covalent geometry    : angle       0.72428 (12233)
  SS BOND              : bond        0.00420 (   17)
  SS BOND              : angle       1.47926 (   34)
  hydrogen bonds       : bond        0.03427 (  119)
  hydrogen bonds       : angle       7.52444 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6449 (mmm160) cc_final: 0.5702 (mmt180)
REVERT: A   90 ASN cc_start: 0.7720 (p0) cc_final: 0.7365 (p0)
REVERT: A  110 MET cc_start: 0.7767 (mmm) cc_final: 0.7361 (mmm)
REVERT: A  329 GLU cc_start: 0.7550 (mp0) cc_final: 0.6948 (mm-30)
REVERT: A  360 LEU cc_start: 0.7682 (mm) cc_final: 0.7006 (tt)
REVERT: A  404 ASP cc_start: 0.8534 (t0) cc_final: 0.8299 (t0)
REVERT: A  513 GLN cc_start: 0.7382 (tp-100) cc_final: 0.6650 (mp10)
REVERT: A  518 PHE cc_start: 0.6356 (t80) cc_final: 0.6153 (t80)
REVERT: A  562 TYR cc_start: 0.6979 (m-80) cc_final: 0.6653 (m-10)
REVERT: A  616 LYS cc_start: 0.8817 (tttp) cc_final: 0.8525 (tppt)
REVERT: A  765 LYS cc_start: 0.7563 (mttp) cc_final: 0.6874 (mttm)
REVERT: A  783 LEU cc_start: 0.8822 (tp) cc_final: 0.8594 (tp)
REVERT: C  403 LEU cc_start: 0.6212 (tp) cc_final: 0.5959 (tt)
REVERT: C  518 PHE cc_start: 0.7356 (t80) cc_final: 0.7068 (t80)
REVERT: C  780 ARG cc_start: 0.6397 (ttt-90) cc_final: 0.5480 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1028
  time to fit residues: 22.0642
Evaluate side-chains
  121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 103 optimal weight:    0.0170
   chunk 100 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 98 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
A 594 ASN
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.193941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.163710 restraints weight = 18846.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.168808 restraints weight = 19331.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.169361 restraints weight = 14796.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.170465 restraints weight = 10431.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.171200 restraints weight = 9372.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6142
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9049  Z= 0.122
  Angle     :  0.720  11.915  12267  Z= 0.362
  Chirality :  0.048   0.199   1337
  Planarity :  0.005   0.053   1568
  Dihedral  :  6.101  25.853   1184
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.80 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.30 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.93 (0.23), residues: 1065
  helix: -2.68 (0.41), residues: 118
  sheet: -2.81 (0.39), residues: 153
  loop : -2.78 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 236 
 TYR   0.027   0.002   TYR A 374 
 PHE   0.026   0.002   PHE C 475 
 TRP   0.017   0.002   TRP C 632 
 HIS   0.022   0.001   HIS C 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9032)
  covalent geometry    : angle       0.71817 (12233)
  SS BOND              : bond        0.00368 (   17)
  SS BOND              : angle       1.18675 (   34)
  hydrogen bonds       : bond        0.03576 (  119)
  hydrogen bonds       : angle       7.32917 (  279)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.6618 (mmm160) cc_final: 0.5742 (mmt180)
REVERT: A   90 ASN cc_start: 0.7638 (p0) cc_final: 0.7344 (p0)
REVERT: A  110 MET cc_start: 0.7677 (mmm) cc_final: 0.7347 (mmm)
REVERT: A  360 LEU cc_start: 0.7644 (mm) cc_final: 0.6935 (tt)
REVERT: A  404 ASP cc_start: 0.8294 (t0) cc_final: 0.8020 (t0)
REVERT: A  513 GLN cc_start: 0.7244 (tp-100) cc_final: 0.6454 (mp10)
REVERT: A  616 LYS cc_start: 0.8712 (tttp) cc_final: 0.8391 (tppt)
REVERT: A  765 LYS cc_start: 0.7057 (mttp) cc_final: 0.6410 (mttm)
REVERT: A  783 LEU cc_start: 0.8818 (tp) cc_final: 0.8589 (tp)
REVERT: C  403 LEU cc_start: 0.6096 (tp) cc_final: 0.5846 (tt)
REVERT: C  552 LEU cc_start: 0.9046 (tp) cc_final: 0.8714 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1086
  time to fit residues: 23.4875
Evaluate side-chains
  120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 7 optimal weight:    0.0070
   chunk 57 optimal weight:    0.3980
   chunk 86 optimal weight:    9.9990
   chunk 54 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0470
   chunk 75 optimal weight:    5.9990
   chunk 91 optimal weight:    0.3980
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
A 295 ASN
A 594 ASN
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.193809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.163214 restraints weight = 18784.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.168704 restraints weight = 19350.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.168868 restraints weight = 14842.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.169719 restraints weight = 10612.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.170596 restraints weight = 9446.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6149
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9049  Z= 0.122
  Angle     :  0.711  12.144  12267  Z= 0.359
  Chirality :  0.048   0.192   1337
  Planarity :  0.005   0.054   1568
  Dihedral  :  5.971  25.500   1184
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.20 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.77 (0.24), residues: 1065
  helix: -2.64 (0.40), residues: 118
  sheet: -2.37 (0.38), residues: 181
  loop : -2.70 (0.21), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 236 
 TYR   0.022   0.001   TYR D  74 
 PHE   0.022   0.002   PHE C 475 
 TRP   0.016   0.002   TRP C 632 
 HIS   0.015   0.001   HIS C 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9032)
  covalent geometry    : angle       0.70941 (12233)
  SS BOND              : bond        0.00364 (   17)
  SS BOND              : angle       1.20044 (   34)
  hydrogen bonds       : bond        0.03503 (  119)
  hydrogen bonds       : angle       7.06186 (  279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1831.36 seconds
wall clock time: 32 minutes 15.13 seconds (1935.13 seconds total)