Starting phenix.real_space_refine
on Wed Sep 17 05:21:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cy1_46004/09_2025/9cy1_46004.map"
  }
  resolution = 3.15
  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=   0.035
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      39      5.16       5
     C    3286      2.51       5
     N     812      2.21       5
     O     889      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5026
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4114
          Classifications: {'peptide': 529}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 19, 'TRANS': 509}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 912
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 1.58, per 1000 atoms: 0.31
  Number of scatterers: 5026
  At special positions: 0
  Unit cell: (61.544, 103.306, 103.306, 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      39     16.00
     O     889      8.00
     N     812      7.00
     C    3286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  26 " - pdb=" SG  CYS B 100 " 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: 0.40
  Conformation dependent library (CDL) restraints added in 195.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 7 sheets defined
      57.6% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 62 through 88
      removed outlier: 4.323A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 117
      removed outlier: 3.519A  pdb=" N   ALA A 112 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
      removed outlier: 3.883A  pdb=" N   PHE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 3.789A  pdb=" N   VAL A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 200
      removed outlier: 3.615A  pdb=" N   PHE A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 216
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 3.732A  pdb=" N   ILE A 221 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 3.756A  pdb=" N   ASN A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 325 through 334
    Processing helix  chain 'A' and resid 335 through 367
      removed outlier: 3.991A  pdb=" N   TYR A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 401
    Processing helix  chain 'A' and resid 403 through 423
    Processing helix  chain 'A' and resid 424 through 427
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.647A  pdb=" N   ASN A 460 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   SER A 461 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.725A  pdb=" N   LYS A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
      removed outlier: 4.241A  pdb=" N   HIS A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   VAL A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 567 through 583
      removed outlier: 3.628A  pdb=" N   HIS A 575 " --> pdb=" O   ALA A 571 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 596
      removed outlier: 3.720A  pdb=" N   ILE A 589 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 651
      removed outlier: 3.733A  pdb=" N   SER A 636 " --> pdb=" O   LEU A 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 95
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491
      removed outlier: 5.759A  pdb=" N   CYS A 489 " --> pdb=" O   CYS A 504 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS A 504 " --> pdb=" O   CYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602
      removed outlier: 6.857A  pdb=" N   THR A 615 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   TRP A 602 " --> pdb=" O   CYS A 613 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   CYS A 613 " --> pdb=" O   TRP A 602 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 11
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17
      removed outlier: 6.792A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.587A  pdb=" N   TRP B  40 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA B  54 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.587A  pdb=" N   TRP B  40 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA B  54 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 113 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1481
        1.34 -     1.46: 1294
        1.46 -     1.58: 2319
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 5152
  Sorted by residual:
  bond pdb=" C   VAL A 189 "
       pdb=" N   PRO A 190 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 2.34e-02 1.83e+03 6.18e+00
  bond pdb=" C   ARG A  93 "
       pdb=" N   PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.33e+00
  bond pdb=" C   ILE A 383 "
       pdb=" N   PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.10e+00
  bond pdb=" CB  THR A 186 "
       pdb=" CG2 THR A 186 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.43e+00
  bond pdb=" C   LEU A 113 "
       pdb=" N   PRO A 114 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.28e-02 6.10e+03 2.19e+00
  ... (remaining 5147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 6851
        2.95 -     5.90: 101
        5.90 -     8.85: 20
        8.85 -    11.80: 0
       11.80 -    14.75: 1
  Bond angle restraints: 6973
  Sorted by residual:
  angle pdb=" N   VAL B  33 "
        pdb=" CA  VAL B  33 "
        pdb=" C   VAL B  33 "
      ideal   model   delta    sigma   weight residual
     111.91  107.73    4.18 8.90e-01 1.26e+00 2.20e+01
  angle pdb=" C   ASP A 197 "
        pdb=" CA  ASP A 197 "
        pdb=" CB  ASP A 197 "
      ideal   model   delta    sigma   weight residual
     109.72  118.38   -8.66 1.92e+00 2.71e-01 2.03e+01
  angle pdb=" CA  LEU A 344 "
        pdb=" CB  LEU A 344 "
        pdb=" CG  LEU A 344 "
      ideal   model   delta    sigma   weight residual
     116.30  131.05  -14.75 3.50e+00 8.16e-02 1.78e+01
  angle pdb=" C   ALA B  18 "
        pdb=" CA  ALA B  18 "
        pdb=" CB  ALA B  18 "
      ideal   model   delta    sigma   weight residual
     115.89  110.42    5.47 1.32e+00 5.74e-01 1.72e+01
  angle pdb=" CA  TYR A 590 "
        pdb=" CB  TYR A 590 "
        pdb=" CG  TYR A 590 "
      ideal   model   delta    sigma   weight residual
     113.90  121.18   -7.28 1.80e+00 3.09e-01 1.64e+01
  ... (remaining 6968 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2658
       16.09 -    32.17: 265
       32.17 -    48.25: 55
       48.25 -    64.34: 6
       64.34 -    80.42: 5
  Dihedral angle restraints: 2989
    sinusoidal: 1136
      harmonic: 1853
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 530 "
           pdb=" CB  CYS A 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.14  -50.86     1      1.00e+01 1.00e-02 3.54e+01
  dihedral pdb=" CA  ASN A 617 "
           pdb=" C   ASN A 617 "
           pdb=" N   SER A 618 "
           pdb=" CA  SER A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.39  -19.61     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   THR A 531 "
           pdb=" CA  THR A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.21   18.79     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 2986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 633
       0.062 -    0.124: 124
       0.124 -    0.187: 18
       0.187 -    0.249: 4
       0.249 -    0.311: 2
  Chirality restraints: 781
  Sorted by residual:
  chirality pdb=" CB  ILE A  47 "
            pdb=" CA  ILE A  47 "
            pdb=" CG1 ILE A  47 "
            pdb=" CG2 ILE A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  PHE A 117 "
            pdb=" N   PHE A 117 "
            pdb=" C   PHE A 117 "
            pdb=" CB  PHE A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  VAL A  66 "
            pdb=" CA  VAL A  66 "
            pdb=" CG1 VAL A  66 "
            pdb=" CG2 VAL A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 778 not shown)

  Planarity restraints: 858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 113 "    0.070 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A 114 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 114 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 114 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 282 "    0.048 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO A 283 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 115 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   VAL B 115 "    0.047 2.00e-02 2.50e+03
        pdb=" O   VAL B 115 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 116 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 855 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1279
        2.80 -     3.32: 4534
        3.32 -     3.85: 8317
        3.85 -     4.37: 9622
        4.37 -     4.90: 16918
  Nonbonded interactions: 40670
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" OE1 GLN A 541 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ASN B  34 "
            pdb=" OG  SER B  57 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OE1 GLN A 348 "
            pdb=" OH  TYR A 640 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   LEU A 346 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" OE1 GLN A 365 "
            pdb=" NZ  LYS A 433 "
     model   vdw
     2.350 3.120
  ... (remaining 40665 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.020
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5159  Z= 0.233
  Angle     :  0.911  14.749   6987  Z= 0.490
  Chirality :  0.054   0.311    781
  Planarity :  0.008   0.105    858
  Dihedral  : 13.400  80.423   1792
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.30), residues: 633
  helix: -0.25 (0.25), residues: 324
  sheet: -0.61 (0.67), residues: 63
  loop : -0.68 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 526 
 TYR   0.033   0.002   TYR A 590 
 PHE   0.040   0.002   PHE A 386 
 TRP   0.008   0.002   TRP A 602 
 HIS   0.006   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5152)
  covalent geometry    : angle       0.90976 ( 6973)
  SS BOND              : bond        0.00379 (    7)
  SS BOND              : angle       1.23131 (   14)
  hydrogen bonds       : bond        0.13698 (  295)
  hydrogen bonds       : angle       7.09302 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  348 GLN cc_start: 0.7589 (tp40) cc_final: 0.7234 (tt0)
REVERT: A  417 MET cc_start: 0.7379 (tpp) cc_final: 0.7113 (tpp)
REVERT: A  557 MET cc_start: 0.7598 (mmp) cc_final: 0.7231 (mmp)
REVERT: A  577 MET cc_start: 0.7272 (ttt) cc_final: 0.7016 (ttp)
REVERT: A  649 LYS cc_start: 0.7703 (tptm) cc_final: 0.7496 (tttt)
REVERT: B   58 TRP cc_start: 0.6691 (m100) cc_final: 0.6166 (m-10)
REVERT: B  108 TYR cc_start: 0.7153 (m-10) cc_final: 0.6912 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0701
  time to fit residues: 11.3910
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
B  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.174772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.137866 restraints weight = 5651.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.04
r_work: 0.3484 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5159  Z= 0.127
  Angle     :  0.526   5.478   6987  Z= 0.282
  Chirality :  0.040   0.131    781
  Planarity :  0.005   0.078    858
  Dihedral  :  4.110  20.566    699
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  7.71 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.32), residues: 633
  helix:  1.20 (0.27), residues: 332
  sheet: -0.19 (0.80), residues: 46
  loop : -0.39 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.025   0.001   TYR A 590 
 PHE   0.018   0.001   PHE A 386 
 TRP   0.004   0.001   TRP A 258 
 HIS   0.002   0.000   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5152)
  covalent geometry    : angle       0.52513 ( 6973)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       0.93157 (   14)
  hydrogen bonds       : bond        0.04125 (  295)
  hydrogen bonds       : angle       4.72462 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7349 (t0) cc_final: 0.7120 (t0)
REVERT: A   46 ILE cc_start: 0.8502 (tp) cc_final: 0.8248 (tp)
REVERT: A   70 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7716 (m-30)
REVERT: A   90 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8200 (mmtm)
REVERT: A  348 GLN cc_start: 0.7766 (tp40) cc_final: 0.7360 (tt0)
REVERT: A  557 MET cc_start: 0.8122 (mmp) cc_final: 0.7669 (mmt)
REVERT: A  577 MET cc_start: 0.8162 (ttt) cc_final: 0.7948 (ttp)
REVERT: A  645 TYR cc_start: 0.7897 (t80) cc_final: 0.7335 (t80)
REVERT: A  649 LYS cc_start: 0.7864 (tptm) cc_final: 0.7298 (tttt)
REVERT: B   58 TRP cc_start: 0.6978 (m100) cc_final: 0.6115 (m-10)
REVERT: B   87 MET cc_start: 0.7922 (mtp) cc_final: 0.7496 (mtm)
REVERT: B   99 TYR cc_start: 0.8364 (m-80) cc_final: 0.7940 (m-80)
REVERT: B  108 TYR cc_start: 0.7911 (m-10) cc_final: 0.7595 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0637
  time to fit residues: 9.2088
Evaluate side-chains
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0370
   chunk 44 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.174217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.137449 restraints weight = 5603.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.02
r_work: 0.3480 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5159  Z= 0.115
  Angle     :  0.489   5.519   6987  Z= 0.262
  Chirality :  0.040   0.220    781
  Planarity :  0.004   0.060    858
  Dihedral  :  3.809  20.125    699
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.83 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.33), residues: 633
  helix:  1.75 (0.28), residues: 333
  sheet:  0.05 (0.83), residues: 46
  loop : -0.34 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 103 
 TYR   0.025   0.001   TYR A 590 
 PHE   0.015   0.001   PHE A 175 
 TRP   0.004   0.001   TRP B  51 
 HIS   0.002   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5152)
  covalent geometry    : angle       0.48836 ( 6973)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       0.76246 (   14)
  hydrogen bonds       : bond        0.03710 (  295)
  hydrogen bonds       : angle       4.36925 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7216 (t0) cc_final: 0.6983 (t0)
REVERT: A   46 ILE cc_start: 0.8538 (tp) cc_final: 0.8298 (tp)
REVERT: A   47 ILE cc_start: 0.8685 (mm) cc_final: 0.8438 (mm)
REVERT: A   70 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7845 (m-30)
REVERT: A   90 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8122 (mmtm)
REVERT: A  348 GLN cc_start: 0.7699 (tp40) cc_final: 0.7295 (tt0)
REVERT: A  421 PHE cc_start: 0.8088 (m-80) cc_final: 0.7784 (m-80)
REVERT: A  432 ASN cc_start: 0.7839 (m-40) cc_final: 0.7472 (m-40)
REVERT: A  557 MET cc_start: 0.8131 (mmp) cc_final: 0.7693 (mmt)
REVERT: A  645 TYR cc_start: 0.7875 (t80) cc_final: 0.7187 (t80)
REVERT: A  649 LYS cc_start: 0.7909 (tptm) cc_final: 0.7455 (tttm)
REVERT: B   58 TRP cc_start: 0.6992 (m100) cc_final: 0.6108 (m-10)
REVERT: B   87 MET cc_start: 0.7982 (mtp) cc_final: 0.7688 (mtm)
REVERT: B  108 TYR cc_start: 0.8032 (m-10) cc_final: 0.7609 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.0579
  time to fit residues: 8.5877
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.172622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135200 restraints weight = 5684.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.06
r_work: 0.3455 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5159  Z= 0.134
  Angle     :  0.503   5.567   6987  Z= 0.271
  Chirality :  0.040   0.150    781
  Planarity :  0.004   0.053    858
  Dihedral  :  3.787  20.443    699
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.29 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.33), residues: 633
  helix:  2.01 (0.28), residues: 333
  sheet:  0.15 (0.84), residues: 46
  loop : -0.44 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.025   0.001   TYR A 590 
 PHE   0.024   0.001   PHE A 386 
 TRP   0.004   0.001   TRP B  40 
 HIS   0.003   0.001   HIS A 520 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5152)
  covalent geometry    : angle       0.50075 ( 6973)
  SS BOND              : bond        0.00292 (    7)
  SS BOND              : angle       1.14078 (   14)
  hydrogen bonds       : bond        0.03807 (  295)
  hydrogen bonds       : angle       4.32508 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.7215 (t0) cc_final: 0.6987 (t0)
REVERT: A   46 ILE cc_start: 0.8576 (tp) cc_final: 0.8340 (tp)
REVERT: A   47 ILE cc_start: 0.8713 (mm) cc_final: 0.8443 (mm)
REVERT: A   60 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8095 (mm-30)
REVERT: A   70 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7851 (m-30)
REVERT: A   90 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8132 (mmtm)
REVERT: A  348 GLN cc_start: 0.7780 (tp40) cc_final: 0.7364 (tt0)
REVERT: A  432 ASN cc_start: 0.7958 (m-40) cc_final: 0.7589 (m-40)
REVERT: A  477 ASN cc_start: 0.7502 (m110) cc_final: 0.7206 (m110)
REVERT: A  536 PHE cc_start: 0.8205 (m-80) cc_final: 0.8002 (m-80)
REVERT: A  557 MET cc_start: 0.8071 (mmp) cc_final: 0.7645 (mmt)
REVERT: A  567 LEU cc_start: 0.8655 (mp) cc_final: 0.8428 (mp)
REVERT: A  649 LYS cc_start: 0.7838 (tptm) cc_final: 0.7429 (tttm)
REVERT: B   58 TRP cc_start: 0.7091 (m100) cc_final: 0.6054 (m-10)
REVERT: B   87 MET cc_start: 0.8007 (mtp) cc_final: 0.7654 (mtm)
REVERT: B  108 TYR cc_start: 0.8122 (m-10) cc_final: 0.7642 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0585
  time to fit residues: 8.7627
Evaluate side-chains
  103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134293 restraints weight = 5737.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.06
r_work: 0.3451 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5159  Z= 0.130
  Angle     :  0.508   8.277   6987  Z= 0.271
  Chirality :  0.040   0.136    781
  Planarity :  0.004   0.049    858
  Dihedral  :  3.802  20.706    699
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.39 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.33), residues: 633
  helix:  2.13 (0.28), residues: 333
  sheet:  0.19 (0.84), residues: 46
  loop : -0.52 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.024   0.001   TYR A 590 
 PHE   0.015   0.001   PHE A 117 
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5152)
  covalent geometry    : angle       0.50347 ( 6973)
  SS BOND              : bond        0.00393 (    7)
  SS BOND              : angle       1.63522 (   14)
  hydrogen bonds       : bond        0.03629 (  295)
  hydrogen bonds       : angle       4.26558 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7268 (t0) cc_final: 0.7037 (t0)
REVERT: A   46 ILE cc_start: 0.8617 (tp) cc_final: 0.8399 (tp)
REVERT: A   47 ILE cc_start: 0.8705 (mm) cc_final: 0.8435 (mm)
REVERT: A   60 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7960 (mm-30)
REVERT: A   70 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7953 (m-30)
REVERT: A   90 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8060 (mmtm)
REVERT: A  348 GLN cc_start: 0.7734 (tp40) cc_final: 0.7315 (tt0)
REVERT: A  432 ASN cc_start: 0.8032 (m-40) cc_final: 0.7687 (m-40)
REVERT: A  557 MET cc_start: 0.8033 (mmp) cc_final: 0.7606 (mmt)
REVERT: A  649 LYS cc_start: 0.7888 (tptm) cc_final: 0.7495 (tttm)
REVERT: B   58 TRP cc_start: 0.7195 (m100) cc_final: 0.6148 (m-10)
REVERT: B   91 LYS cc_start: 0.8100 (mttm) cc_final: 0.7887 (mttm)
REVERT: B  108 TYR cc_start: 0.8195 (m-80) cc_final: 0.7645 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0656
  time to fit residues: 9.3684
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.170696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133256 restraints weight = 5815.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.08
r_work: 0.3430 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.132
  Angle     :  0.499   5.598   6987  Z= 0.265
  Chirality :  0.040   0.138    781
  Planarity :  0.004   0.046    858
  Dihedral  :  3.739  20.648    699
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.94 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.33), residues: 633
  helix:  2.13 (0.28), residues: 333
  sheet:  0.05 (0.83), residues: 46
  loop : -0.52 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  71 
 TYR   0.024   0.001   TYR A 590 
 PHE   0.026   0.001   PHE A 386 
 TRP   0.005   0.001   TRP B  40 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5152)
  covalent geometry    : angle       0.49536 ( 6973)
  SS BOND              : bond        0.00217 (    7)
  SS BOND              : angle       1.49542 (   14)
  hydrogen bonds       : bond        0.03637 (  295)
  hydrogen bonds       : angle       4.25548 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7272 (t0) cc_final: 0.7044 (t0)
REVERT: A   47 ILE cc_start: 0.8689 (mm) cc_final: 0.8397 (mm)
REVERT: A   60 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7991 (mm-30)
REVERT: A   70 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7907 (m-30)
REVERT: A  348 GLN cc_start: 0.7717 (tp40) cc_final: 0.7304 (tt0)
REVERT: A  432 ASN cc_start: 0.8039 (m-40) cc_final: 0.7705 (m-40)
REVERT: A  557 MET cc_start: 0.8068 (mmp) cc_final: 0.7630 (mmp)
REVERT: A  649 LYS cc_start: 0.7881 (tptm) cc_final: 0.7479 (tttm)
REVERT: B   58 TRP cc_start: 0.7204 (m100) cc_final: 0.6142 (m-10)
REVERT: B   91 LYS cc_start: 0.8094 (mttm) cc_final: 0.7887 (mttm)
REVERT: B  108 TYR cc_start: 0.8294 (m-80) cc_final: 0.7703 (m-80)
  outliers start: 15
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0668
  time to fit residues: 9.5790
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0370
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.171003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.133915 restraints weight = 5757.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.06
r_work: 0.3435 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.121
  Angle     :  0.506   9.346   6987  Z= 0.263
  Chirality :  0.039   0.136    781
  Planarity :  0.004   0.045    858
  Dihedral  :  3.696  20.884    699
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.96 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.33), residues: 633
  helix:  2.15 (0.28), residues: 333
  sheet:  0.06 (0.82), residues: 46
  loop : -0.54 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.023   0.001   TYR A 590 
 PHE   0.026   0.001   PHE A 386 
 TRP   0.005   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5152)
  covalent geometry    : angle       0.50364 ( 6973)
  SS BOND              : bond        0.00232 (    7)
  SS BOND              : angle       1.22684 (   14)
  hydrogen bonds       : bond        0.03547 (  295)
  hydrogen bonds       : angle       4.23357 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7235 (t0) cc_final: 0.7005 (t0)
REVERT: A   47 ILE cc_start: 0.8698 (mm) cc_final: 0.8408 (mm)
REVERT: A   60 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7944 (mm-30)
REVERT: A   70 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7922 (m-30)
REVERT: A  348 GLN cc_start: 0.7669 (tp40) cc_final: 0.7258 (tt0)
REVERT: A  432 ASN cc_start: 0.7959 (m-40) cc_final: 0.7710 (m-40)
REVERT: A  477 ASN cc_start: 0.7582 (m-40) cc_final: 0.7350 (m110)
REVERT: A  557 MET cc_start: 0.8058 (mmp) cc_final: 0.7858 (mmp)
REVERT: A  649 LYS cc_start: 0.7895 (tptm) cc_final: 0.7511 (tttm)
REVERT: B   58 TRP cc_start: 0.7223 (m100) cc_final: 0.6120 (m-10)
REVERT: B  108 TYR cc_start: 0.8293 (m-80) cc_final: 0.7729 (m-80)
  outliers start: 14
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0624
  time to fit residues: 9.3305
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133006 restraints weight = 5731.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.04
r_work: 0.3436 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5159  Z= 0.135
  Angle     :  0.513   8.462   6987  Z= 0.266
  Chirality :  0.040   0.137    781
  Planarity :  0.004   0.045    858
  Dihedral  :  3.738  21.020    699
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.33 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.33), residues: 633
  helix:  2.14 (0.28), residues: 333
  sheet:  0.09 (0.81), residues: 46
  loop : -0.54 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.027   0.002   TYR A  86 
 PHE   0.026   0.001   PHE A 386 
 TRP   0.006   0.001   TRP B  40 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5152)
  covalent geometry    : angle       0.51050 ( 6973)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       1.21215 (   14)
  hydrogen bonds       : bond        0.03639 (  295)
  hydrogen bonds       : angle       4.25479 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7192 (t0) cc_final: 0.6968 (t0)
REVERT: A   47 ILE cc_start: 0.8707 (mm) cc_final: 0.8406 (mm)
REVERT: A   60 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8016 (mm-30)
REVERT: A   70 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7887 (m-30)
REVERT: A  348 GLN cc_start: 0.7730 (tp40) cc_final: 0.7303 (tt0)
REVERT: A  421 PHE cc_start: 0.8239 (m-80) cc_final: 0.7947 (m-80)
REVERT: A  432 ASN cc_start: 0.7941 (m-40) cc_final: 0.7674 (m-40)
REVERT: A  557 MET cc_start: 0.8047 (mmp) cc_final: 0.7846 (mmp)
REVERT: A  614 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8116 (mmt90)
REVERT: A  649 LYS cc_start: 0.7869 (tptm) cc_final: 0.7482 (tttm)
REVERT: B   58 TRP cc_start: 0.7273 (m100) cc_final: 0.6229 (m-10)
REVERT: B   91 LYS cc_start: 0.8112 (mttm) cc_final: 0.7822 (mtmm)
REVERT: B  108 TYR cc_start: 0.8332 (m-80) cc_final: 0.7789 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 103
  average time/residue: 0.0618
  time to fit residues: 8.7287
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    0.3980
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.169627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.132383 restraints weight = 5723.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.04
r_work: 0.3426 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5159  Z= 0.135
  Angle     :  0.510   8.437   6987  Z= 0.265
  Chirality :  0.040   0.138    781
  Planarity :  0.004   0.044    858
  Dihedral  :  3.717  20.934    699
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.70 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.33), residues: 633
  helix:  2.13 (0.28), residues: 333
  sheet:  0.02 (0.81), residues: 46
  loop : -0.53 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.027   0.001   TYR A  86 
 PHE   0.027   0.001   PHE A 386 
 TRP   0.007   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5152)
  covalent geometry    : angle       0.50770 ( 6973)
  SS BOND              : bond        0.00222 (    7)
  SS BOND              : angle       1.16772 (   14)
  hydrogen bonds       : bond        0.03633 (  295)
  hydrogen bonds       : angle       4.25315 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7346 (t0) cc_final: 0.7110 (t0)
REVERT: A   47 ILE cc_start: 0.8688 (mm) cc_final: 0.8379 (mm)
REVERT: A   60 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8056 (mm-30)
REVERT: A   70 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7913 (m-30)
REVERT: A  348 GLN cc_start: 0.7773 (tp40) cc_final: 0.7347 (tt0)
REVERT: A  432 ASN cc_start: 0.7920 (m-40) cc_final: 0.7654 (m-40)
REVERT: A  557 MET cc_start: 0.8051 (mmp) cc_final: 0.7844 (mmp)
REVERT: A  567 LEU cc_start: 0.8783 (mp) cc_final: 0.8520 (mt)
REVERT: A  614 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8236 (mmt90)
REVERT: A  649 LYS cc_start: 0.7883 (tptm) cc_final: 0.7474 (tttm)
REVERT: B   58 TRP cc_start: 0.7296 (m100) cc_final: 0.6254 (m-10)
REVERT: B   91 LYS cc_start: 0.8148 (mttm) cc_final: 0.7846 (mtmm)
REVERT: B  108 TYR cc_start: 0.8375 (m-80) cc_final: 0.7758 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 106
  average time/residue: 0.0643
  time to fit residues: 9.3845
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0770
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.4338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.163601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129610 restraints weight = 5905.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.89
r_work: 0.3271 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5159  Z= 0.108
  Angle     :  0.497   8.072   6987  Z= 0.260
  Chirality :  0.039   0.133    781
  Planarity :  0.004   0.045    858
  Dihedral  :  3.616  21.308    699
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.88 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.33), residues: 633
  helix:  2.24 (0.28), residues: 333
  sheet:  0.09 (0.81), residues: 46
  loop : -0.50 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.023   0.001   TYR A 590 
 PHE   0.027   0.001   PHE A 386 
 TRP   0.007   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5152)
  covalent geometry    : angle       0.49526 ( 6973)
  SS BOND              : bond        0.00196 (    7)
  SS BOND              : angle       1.05318 (   14)
  hydrogen bonds       : bond        0.03406 (  295)
  hydrogen bonds       : angle       4.17020 (  879)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   25 ASN cc_start: 0.7014 (t0) cc_final: 0.6786 (t0)
REVERT: A   48 MET cc_start: 0.9012 (tpp) cc_final: 0.8702 (tpp)
REVERT: A   60 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7953 (mm-30)
REVERT: A   70 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7909 (m-30)
REVERT: A  180 LEU cc_start: 0.8172 (tp) cc_final: 0.7957 (mp)
REVERT: A  348 GLN cc_start: 0.7677 (tp40) cc_final: 0.7276 (tt0)
REVERT: A  421 PHE cc_start: 0.8232 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  432 ASN cc_start: 0.7752 (m-40) cc_final: 0.7548 (m-40)
REVERT: A  567 LEU cc_start: 0.8789 (mp) cc_final: 0.8531 (mt)
REVERT: A  614 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8232 (mmt90)
REVERT: A  649 LYS cc_start: 0.7915 (tptm) cc_final: 0.7539 (tttm)
REVERT: B   58 TRP cc_start: 0.7271 (m100) cc_final: 0.6236 (m-10)
REVERT: B   91 LYS cc_start: 0.8203 (mttm) cc_final: 0.7895 (mtmm)
REVERT: B  108 TYR cc_start: 0.8262 (m-80) cc_final: 0.7681 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0653
  time to fit residues: 9.6356
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0870
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7960

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.161094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.126383 restraints weight = 5930.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.91
r_work: 0.3228 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5159  Z= 0.136
  Angle     :  0.529   8.078   6987  Z= 0.274
  Chirality :  0.040   0.151    781
  Planarity :  0.004   0.044    858
  Dihedral  :  3.686  21.578    699
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.06 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.33), residues: 633
  helix:  2.19 (0.28), residues: 333
  sheet:  0.04 (0.82), residues: 46
  loop : -0.55 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  71 
 TYR   0.024   0.001   TYR A 590 
 PHE   0.028   0.002   PHE A 386 
 TRP   0.007   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5152)
  covalent geometry    : angle       0.52395 ( 6973)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       1.69423 (   14)
  hydrogen bonds       : bond        0.03642 (  295)
  hydrogen bonds       : angle       4.22212 (  879)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1536.89 seconds
wall clock time: 27 minutes 7.56 seconds (1627.56 seconds total)