Starting phenix.real_space_refine
on Sat May 10 08:38:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sno_40631/05_2025/8sno_40631.cif"
  }
  resolution = 2.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      55      5.16       5
     C    3635      2.51       5
     N     961      2.21       5
     O    1033      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5685
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1745
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3939
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.07, per 1000 atoms: 0.72
  Number of scatterers: 5685
  At special positions: 0
  Unit cell: (72.6264, 85.0059, 134.524, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      55     16.00
     O    1033      8.00
     N     961      7.00
     C    3635      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 478 " - pdb=" SG  CYS A 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 501 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 514 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 521 " - pdb=" SG  CYS A 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 555 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 573 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 567 " - pdb=" SG  CYS A 578 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 582 " - pdb=" SG  CYS A 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 591 " - pdb=" SG  CYS A 611 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS A 603 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 635 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 641 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 447 " - pdb=" SG  CYS B 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 470 " - pdb=" SG  CYS B 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 487 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 479 " - pdb=" SG  CYS B 564 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 527 " - pdb=" SG  CYS B 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 571 " - pdb=" SG  CYS B 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 572 " - pdb=" SG  CYS B 606 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 579 " - pdb=" SG  CYS B 601 " distance=2.04

  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: 1.26
  Conformation dependent library (CDL) restraints added in 629.0 milliseconds
  

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      45.3% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 580 through 585
      removed outlier: 3.584A  pdb=" N   ARG A 584 " --> pdb=" O   PRO A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 599
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.554A  pdb=" N   GLN A 658 " --> pdb=" O   ASP A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 670
    Processing helix  chain 'A' and resid 671 through 703
      Proline residue:  A 686  - end of helix
    Processing helix  chain 'B' and resid 344 through 349
    Processing helix  chain 'B' and resid 358 through 367
    Processing helix  chain 'B' and resid 373 through 394
    Processing helix  chain 'B' and resid 433 through 441
    Processing helix  chain 'B' and resid 444 through 449
    Processing helix  chain 'B' and resid 452 through 467
      removed outlier: 3.965A  pdb=" N   ASP B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 487
    Processing helix  chain 'B' and resid 541 through 545
    Processing helix  chain 'B' and resid 583 through 590
    Processing helix  chain 'B' and resid 600 through 604
    Processing helix  chain 'B' and resid 605 through 612
      removed outlier: 3.931A  pdb=" N   LYS B 609 " --> pdb=" O   HIS B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 631
    Processing helix  chain 'B' and resid 637 through 659
      removed outlier: 3.541A  pdb=" N   LEU B 652 " --> pdb=" O   GLN B 648 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   ARG B 653 " --> pdb=" O   MET B 649 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASP B 654 " --> pdb=" O   THR B 650 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 683
    Processing helix  chain 'B' and resid 691 through 709
    Processing helix  chain 'B' and resid 710 through 713
    Processing helix  chain 'B' and resid 715 through 734
      removed outlier: 3.913A  pdb=" N   ALA B 719 " --> pdb=" O   ARG B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 756
      removed outlier: 3.682A  pdb=" N   HIS B 744 " --> pdb=" O   ASP B 740 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE B 756 " --> pdb=" O   LEU B 752 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 766 through 796
      removed outlier: 3.982A  pdb=" N   TYR B 770 " --> pdb=" O   THR B 766 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 801 through 803
      No H-bonds generated for 'chain 'B' and resid 801 through 803'
    Processing helix  chain 'B' and resid 804 through 809
      removed outlier: 3.965A  pdb=" N   THR B 808 " --> pdb=" O   ILE B 804 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 821
    Processing sheet with id=AA1, first strand: chain 'A' and resid 522 through 523
    Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535
      removed outlier: 3.514A  pdb=" N   GLN A 535 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
    Processing sheet with id=AA4, first strand: chain 'A' and resid 590 through 591
      removed outlier: 4.330A  pdb=" N   CYS A 603 " --> pdb=" O   CYS A 591 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 633 through 634
    Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 411
    Processing sheet with id=AA7, first strand: chain 'B' and resid 481 through 482
    Processing sheet with id=AA8, first strand: chain 'B' and resid 527 through 529
      removed outlier: 6.556A  pdb=" N   GLU B 550 " --> pdb=" O   GLU B 528 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 579 through 582

    238 hydrogen bonds defined for protein.
    660 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: 1.56

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1505
        1.33 -     1.45: 1108
        1.45 -     1.57: 3154
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 5828
  Sorted by residual:
  bond pdb=" CA  ALA B 518 "
       pdb=" C   ALA B 518 "
    ideal  model  delta    sigma   weight residual
    1.529  1.494  0.035 1.04e-02 9.25e+03 1.14e+01
  bond pdb=" CA  VAL A 483 "
       pdb=" C   VAL A 483 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.037 1.22e-02 6.72e+03 9.31e+00
  bond pdb=" N   ALA B 518 "
       pdb=" CA  ALA B 518 "
    ideal  model  delta    sigma   weight residual
    1.462  1.430  0.032 1.32e-02 5.74e+03 5.96e+00
  bond pdb=" C   PRO B 503 "
       pdb=" O   PRO B 503 "
    ideal  model  delta    sigma   weight residual
    1.240  1.215  0.025 1.12e-02 7.97e+03 5.18e+00
  bond pdb=" C   VAL B 519 "
       pdb=" O   VAL B 519 "
    ideal  model  delta    sigma   weight residual
    1.239  1.212  0.027 1.22e-02 6.72e+03 4.97e+00
  ... (remaining 5823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 7775
        2.41 -     4.83: 117
        4.83 -     7.24: 10
        7.24 -     9.66: 3
        9.66 -    12.07: 2
  Bond angle restraints: 7907
  Sorted by residual:
  angle pdb=" C   VAL A 483 "
        pdb=" CA  VAL A 483 "
        pdb=" CB  VAL A 483 "
      ideal   model   delta    sigma   weight residual
     111.28  101.24   10.04 1.38e+00 5.25e-01 5.30e+01
  angle pdb=" N   ALA B 518 "
        pdb=" CA  ALA B 518 "
        pdb=" C   ALA B 518 "
      ideal   model   delta    sigma   weight residual
     107.20   95.13   12.07 1.70e+00 3.46e-01 5.04e+01
  angle pdb=" N   SER B 516 "
        pdb=" CA  SER B 516 "
        pdb=" C   SER B 516 "
      ideal   model   delta    sigma   weight residual
     107.99  115.29   -7.30 1.76e+00 3.23e-01 1.72e+01
  angle pdb=" N   CYS A 567 "
        pdb=" CA  CYS A 567 "
        pdb=" C   CYS A 567 "
      ideal   model   delta    sigma   weight residual
     109.31  114.92   -5.61 1.42e+00 4.96e-01 1.56e+01
  angle pdb=" C   CYS A 567 "
        pdb=" CA  CYS A 567 "
        pdb=" CB  CYS A 567 "
      ideal   model   delta    sigma   weight residual
     114.16  105.84    8.32 2.31e+00 1.87e-01 1.30e+01
  ... (remaining 7902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 3151
       16.25 -    32.50: 271
       32.50 -    48.74: 67
       48.74 -    64.99: 10
       64.99 -    81.24: 6
  Dihedral angle restraints: 3505
    sinusoidal: 1429
      harmonic: 2076
  Sorted by residual:
  dihedral pdb=" CB  CYS A 489 "
           pdb=" SG  CYS A 489 "
           pdb=" SG  CYS A 502 "
           pdb=" CB  CYS A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.38   62.38     1      1.00e+01 1.00e-02 5.15e+01
  dihedral pdb=" CB  CYS A 591 "
           pdb=" SG  CYS A 591 "
           pdb=" SG  CYS A 611 "
           pdb=" CB  CYS A 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.79   41.79     1      1.00e+01 1.00e-02 2.44e+01
  dihedral pdb=" CB  CYS A 542 "
           pdb=" SG  CYS A 542 "
           pdb=" SG  CYS A 573 "
           pdb=" CB  CYS A 573 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.38  -38.38     1      1.00e+01 1.00e-02 2.07e+01
  ... (remaining 3502 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 655
       0.044 -    0.089: 162
       0.089 -    0.133: 46
       0.133 -    0.177: 1
       0.177 -    0.222: 4
  Chirality restraints: 868
  Sorted by residual:
  chirality pdb=" CA  SER B 516 "
            pdb=" N   SER B 516 "
            pdb=" C   SER B 516 "
            pdb=" CB  SER B 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ALA B 518 "
            pdb=" N   ALA B 518 "
            pdb=" C   ALA B 518 "
            pdb=" CB  ALA B 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.69   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  VAL A 483 "
            pdb=" CA  VAL A 483 "
            pdb=" CG1 VAL A 483 "
            pdb=" CG2 VAL A 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 865 not shown)

  Planarity restraints: 1015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 517 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.18e+00
        pdb=" C   GLY B 517 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLY B 517 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ALA B 518 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 516 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.96e+00
        pdb=" C   SER B 516 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   SER B 516 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY B 517 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 372 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 373 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1012 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 114
        2.68 -     3.24: 5579
        3.24 -     3.79: 8926
        3.79 -     4.35: 12282
        4.35 -     4.90: 20061
  Nonbonded interactions: 46962
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 465 "
            pdb=" OG  SER B 602 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG1 THR B 376 "
            pdb=" OE1 GLU B 656 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASN A 480 "
            pdb="CA    CA A 901 "
     model   vdw
     2.257 2.510
  nonbonded pdb=" O   VAL A 477 "
            pdb="CA    CA A 901 "
     model   vdw
     2.268 2.510
  nonbonded pdb=" NE2 GLN B 522 "
            pdb=" O   PRO B 546 "
     model   vdw
     2.322 3.120
  ... (remaining 46957 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:             8.850
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     17.100
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
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      :  0.004   0.045   5849  Z= 0.240
  Angle     :  0.712  12.070   7949  Z= 0.420
  Chirality :  0.044   0.222    868
  Planarity :  0.004   0.036   1015
  Dihedral  : 12.789  81.238   2102
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.32), residues: 714
  helix:  1.11 (0.32), residues: 286
  sheet: -0.86 (0.84), residues: 45
  loop : -0.89 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.006   0.001   HIS B 561 
 PHE   0.011   0.001   PHE B 668 
 TYR   0.012   0.001   TYR B 770 
 ARG   0.003   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17595 (  238)
  hydrogen bonds       : angle       6.12331 (  660)
  SS BOND              : bond        0.00383 (   21)
  SS BOND              : angle       1.49601 (   42)
  covalent geometry    : bond        0.00399 ( 5828)
  covalent geometry    : angle       0.70562 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.611 
Fit side-chains
REVERT: B  408 GLN cc_start: 0.7540 (mt0) cc_final: 0.7202 (mt0)
REVERT: B  455 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6421 (tp30)
REVERT: B  459 LEU cc_start: 0.8318 (mp) cc_final: 0.7925 (mp)
REVERT: B  728 LEU cc_start: 0.7612 (tp) cc_final: 0.7393 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 1.0014
  time to fit residues: 86.8263
Evaluate side-chains
  54 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.161853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120036 restraints weight = 6378.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.85
r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5849  Z= 0.139
  Angle     :  0.555   6.735   7949  Z= 0.290
  Chirality :  0.041   0.125    868
  Planarity :  0.004   0.041   1015
  Dihedral  :  4.394  20.837    768
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  7.45 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.32), residues: 714
  helix:  1.68 (0.31), residues: 282
  sheet: -0.82 (0.83), residues: 41
  loop : -0.56 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.006   0.001   HIS B 521 
 PHE   0.015   0.001   PHE B 668 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.005   0.000   ARG A 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04412 (  238)
  hydrogen bonds       : angle       4.59646 (  660)
  SS BOND              : bond        0.00248 (   21)
  SS BOND              : angle       1.29590 (   42)
  covalent geometry    : bond        0.00326 ( 5828)
  covalent geometry    : angle       0.54862 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: A  494 MET cc_start: 0.8211 (ttp) cc_final: 0.7955 (ttp)
REVERT: A  577 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6829 (tppp)
REVERT: B  507 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6432 (mmpt)
REVERT: B  728 LEU cc_start: 0.7833 (tp) cc_final: 0.7559 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 68
  average time/residue: 0.9246
  time to fit residues: 67.0141
Evaluate side-chains
  50 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  724 SER
Chi-restraints excluded: chain B residue  749 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 68 optimal weight:    0.0670
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 ASN
B 551 GLN
B 741 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.158853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.115696 restraints weight = 6441.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.91
r_work: 0.3267 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5849  Z= 0.155
  Angle     :  0.541   5.889   7949  Z= 0.283
  Chirality :  0.041   0.129    868
  Planarity :  0.004   0.042   1015
  Dihedral  :  4.373  21.663    768
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.19 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.32), residues: 714
  helix:  1.58 (0.31), residues: 285
  sheet: -1.03 (0.78), residues: 45
  loop : -0.54 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 629 
 HIS   0.005   0.001   HIS B 521 
 PHE   0.014   0.001   PHE B 696 
 TYR   0.010   0.001   TYR B 593 
 ARG   0.004   0.001   ARG A 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04535 (  238)
  hydrogen bonds       : angle       4.45222 (  660)
  SS BOND              : bond        0.00258 (   21)
  SS BOND              : angle       1.13663 (   42)
  covalent geometry    : bond        0.00371 ( 5828)
  covalent geometry    : angle       0.53575 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  577 LYS cc_start: 0.7093 (ttpt) cc_final: 0.6626 (tppp)
REVERT: B  507 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6481 (tppt)
REVERT: B  724 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7870 (m)
REVERT: B  728 LEU cc_start: 0.7939 (tp) cc_final: 0.7646 (tp)
REVERT: B  819 LYS cc_start: 0.6918 (mtpp) cc_final: 0.6666 (mtpp)
  outliers start: 13
  outliers final: 6
  residues processed: 60
  average time/residue: 0.8668
  time to fit residues: 55.7904
Evaluate side-chains
  53 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  724 SER
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  823 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 42 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0770
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3883 r_free = 0.3883 target = 0.159703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.118867 restraints weight = 6507.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.01
r_work: 0.3265 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5849  Z= 0.127
  Angle     :  0.499   6.586   7949  Z= 0.260
  Chirality :  0.040   0.126    868
  Planarity :  0.004   0.039   1015
  Dihedral  :  4.268  21.654    768
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.14 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.32), residues: 714
  helix:  1.68 (0.31), residues: 286
  sheet: -1.04 (0.73), residues: 50
  loop : -0.50 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 521 
 PHE   0.013   0.001   PHE B 668 
 TYR   0.009   0.001   TYR B 593 
 ARG   0.003   0.000   ARG A 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  238)
  hydrogen bonds       : angle       4.26684 (  660)
  SS BOND              : bond        0.00231 (   21)
  SS BOND              : angle       0.84099 (   42)
  covalent geometry    : bond        0.00300 ( 5828)
  covalent geometry    : angle       0.49606 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  577 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6765 (tppp)
REVERT: A  612 VAL cc_start: 0.8520 (t) cc_final: 0.8296 (p)
REVERT: B  505 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7405 (ttt)
REVERT: B  507 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6498 (tppt)
REVERT: B  728 LEU cc_start: 0.7989 (tp) cc_final: 0.7679 (tp)
REVERT: B  819 LYS cc_start: 0.6972 (mtpp) cc_final: 0.6757 (mtpp)
  outliers start: 14
  outliers final: 6
  residues processed: 66
  average time/residue: 0.7900
  time to fit residues: 56.1033
Evaluate side-chains
  54 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  505 MET
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  823 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3873 r_free = 0.3873 target = 0.158503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.117921 restraints weight = 6491.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.92
r_work: 0.3281 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5849  Z= 0.156
  Angle     :  0.528   6.912   7949  Z= 0.275
  Chirality :  0.041   0.125    868
  Planarity :  0.004   0.040   1015
  Dihedral  :  4.372  21.968    768
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.94 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.32), residues: 714
  helix:  1.58 (0.31), residues: 286
  sheet: -1.20 (0.73), residues: 50
  loop : -0.52 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 629 
 HIS   0.005   0.001   HIS B 662 
 PHE   0.014   0.001   PHE B 696 
 TYR   0.011   0.001   TYR B 593 
 ARG   0.003   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  238)
  hydrogen bonds       : angle       4.30454 (  660)
  SS BOND              : bond        0.00261 (   21)
  SS BOND              : angle       0.92691 (   42)
  covalent geometry    : bond        0.00376 ( 5828)
  covalent geometry    : angle       0.52530 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A  577 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6852 (tppp)
REVERT: A  588 LEU cc_start: 0.8273 (mt) cc_final: 0.8049 (mt)
REVERT: A  612 VAL cc_start: 0.8612 (t) cc_final: 0.8389 (p)
REVERT: A  637 MET cc_start: 0.7951 (pmm) cc_final: 0.6769 (mmm)
REVERT: B  408 GLN cc_start: 0.7719 (mt0) cc_final: 0.7206 (mt0)
REVERT: B  505 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7566 (ttt)
REVERT: B  507 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6395 (tppt)
REVERT: B  565 GLU cc_start: 0.7717 (mp0) cc_final: 0.7452 (mt-10)
REVERT: B  596 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7032 (tm-30)
REVERT: B  724 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7906 (m)
REVERT: B  728 LEU cc_start: 0.8048 (tp) cc_final: 0.7753 (tp)
REVERT: B  819 LYS cc_start: 0.6936 (mtpp) cc_final: 0.6685 (mtpp)
  outliers start: 18
  outliers final: 9
  residues processed: 70
  average time/residue: 0.7692
  time to fit residues: 57.9930
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  505 MET
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  823 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.0010
   chunk 38 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0470
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.2884

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3904 r_free = 0.3904 target = 0.161490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121173 restraints weight = 6392.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.94
r_work: 0.3330 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5849  Z= 0.102
  Angle     :  0.473   6.149   7949  Z= 0.246
  Chirality :  0.039   0.128    868
  Planarity :  0.003   0.037   1015
  Dihedral  :  4.172  21.637    768
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.57 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.32), residues: 714
  helix:  1.85 (0.31), residues: 285
  sheet: -1.02 (0.78), residues: 46
  loop : -0.44 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.002   0.001   HIS B 561 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.007   0.001   TYR B 593 
 ARG   0.001   0.000   ARG B 569 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  238)
  hydrogen bonds       : angle       4.11865 (  660)
  SS BOND              : bond        0.00180 (   21)
  SS BOND              : angle       0.69635 (   42)
  covalent geometry    : bond        0.00234 ( 5828)
  covalent geometry    : angle       0.47152 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A  577 LYS cc_start: 0.7244 (ttpt) cc_final: 0.6780 (tppp)
REVERT: A  612 VAL cc_start: 0.8673 (t) cc_final: 0.8471 (p)
REVERT: A  637 MET cc_start: 0.7864 (pmm) cc_final: 0.6817 (mmm)
REVERT: B  352 SER cc_start: 0.8699 (p) cc_final: 0.8376 (t)
REVERT: B  408 GLN cc_start: 0.7676 (mt0) cc_final: 0.7410 (mt0)
REVERT: B  507 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6352 (tppt)
REVERT: B  596 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6891 (tm-30)
REVERT: B  724 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7857 (m)
REVERT: B  728 LEU cc_start: 0.8074 (tp) cc_final: 0.7756 (tp)
REVERT: B  819 LYS cc_start: 0.6898 (mtpp) cc_final: 0.6673 (mtpp)
  outliers start: 16
  outliers final: 8
  residues processed: 65
  average time/residue: 0.7941
  time to fit residues: 55.7184
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  507 LYS
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Chi-restraints excluded: chain B residue  823 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 741 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.160222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.119810 restraints weight = 6442.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.91
r_work: 0.3311 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5849  Z= 0.123
  Angle     :  0.499   5.921   7949  Z= 0.259
  Chirality :  0.040   0.128    868
  Planarity :  0.004   0.037   1015
  Dihedral  :  4.216  21.478    768
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.04 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.32), residues: 714
  helix:  1.80 (0.31), residues: 285
  sheet: -1.18 (0.73), residues: 50
  loop : -0.49 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 662 
 PHE   0.013   0.001   PHE B 668 
 TYR   0.009   0.001   TYR B 593 
 ARG   0.002   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  238)
  hydrogen bonds       : angle       4.14734 (  660)
  SS BOND              : bond        0.00218 (   21)
  SS BOND              : angle       0.73198 (   42)
  covalent geometry    : bond        0.00290 ( 5828)
  covalent geometry    : angle       0.49719 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  577 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6789 (tppp)
REVERT: B  352 SER cc_start: 0.8704 (p) cc_final: 0.8349 (t)
REVERT: B  408 GLN cc_start: 0.7690 (mt0) cc_final: 0.7405 (mt0)
REVERT: B  505 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7086 (ttt)
REVERT: B  565 GLU cc_start: 0.7614 (mp0) cc_final: 0.7332 (mt-10)
REVERT: B  596 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6853 (tm-30)
REVERT: B  724 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7888 (m)
REVERT: B  819 LYS cc_start: 0.6825 (mtpp) cc_final: 0.6614 (mtpp)
  outliers start: 15
  outliers final: 10
  residues processed: 61
  average time/residue: 0.7141
  time to fit residues: 47.2938
Evaluate side-chains
  59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  505 MET
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Chi-restraints excluded: chain B residue  823 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0040
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3874 r_free = 0.3874 target = 0.158601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117599 restraints weight = 6332.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.93
r_work: 0.3279 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5849  Z= 0.149
  Angle     :  0.530   8.744   7949  Z= 0.275
  Chirality :  0.041   0.122    868
  Planarity :  0.004   0.038   1015
  Dihedral  :  4.352  21.587    768
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.68 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.32), residues: 714
  helix:  1.65 (0.31), residues: 285
  sheet: -1.09 (0.73), residues: 50
  loop : -0.50 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 629 
 HIS   0.005   0.001   HIS B 662 
 PHE   0.014   0.001   PHE B 696 
 TYR   0.011   0.001   TYR B 593 
 ARG   0.003   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  238)
  hydrogen bonds       : angle       4.24062 (  660)
  SS BOND              : bond        0.00235 (   21)
  SS BOND              : angle       0.81952 (   42)
  covalent geometry    : bond        0.00359 ( 5828)
  covalent geometry    : angle       0.52768 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  577 LYS cc_start: 0.7411 (ttpt) cc_final: 0.6946 (tppp)
REVERT: A  588 LEU cc_start: 0.8223 (mt) cc_final: 0.8016 (mt)
REVERT: A  637 MET cc_start: 0.7843 (pmm) cc_final: 0.6938 (mmm)
REVERT: B  352 SER cc_start: 0.8687 (p) cc_final: 0.8313 (t)
REVERT: B  408 GLN cc_start: 0.7698 (mt0) cc_final: 0.7388 (mt0)
REVERT: B  565 GLU cc_start: 0.7744 (mp0) cc_final: 0.7459 (mt-10)
REVERT: B  596 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6847 (tm-30)
REVERT: B  724 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7905 (m)
REVERT: B  728 LEU cc_start: 0.8179 (tp) cc_final: 0.7959 (tp)
REVERT: B  819 LYS cc_start: 0.6893 (mtpp) cc_final: 0.6675 (mtpp)
  outliers start: 15
  outliers final: 10
  residues processed: 62
  average time/residue: 0.7557
  time to fit residues: 51.0674
Evaluate side-chains
  58 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 40 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0270
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3840 r_free = 0.3840 target = 0.157587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.115802 restraints weight = 6450.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.01
r_work: 0.3246 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5849  Z= 0.128
  Angle     :  0.504   8.176   7949  Z= 0.262
  Chirality :  0.040   0.120    868
  Planarity :  0.004   0.037   1015
  Dihedral  :  4.286  21.763    768
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.84 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.32), residues: 714
  helix:  1.72 (0.31), residues: 285
  sheet: -1.02 (0.73), residues: 50
  loop : -0.51 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 662 
 PHE   0.013   0.001   PHE B 668 
 TYR   0.009   0.001   TYR B 593 
 ARG   0.002   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  238)
  hydrogen bonds       : angle       4.17715 (  660)
  SS BOND              : bond        0.00200 (   21)
  SS BOND              : angle       0.78845 (   42)
  covalent geometry    : bond        0.00304 ( 5828)
  covalent geometry    : angle       0.50237 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  495 TYR cc_start: 0.7751 (m-80) cc_final: 0.7191 (m-80)
REVERT: A  577 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6831 (tppp)
REVERT: A  583 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6801 (mp0)
REVERT: A  637 MET cc_start: 0.7764 (pmm) cc_final: 0.6960 (mmm)
REVERT: B  352 SER cc_start: 0.8720 (p) cc_final: 0.8350 (t)
REVERT: B  408 GLN cc_start: 0.7707 (mt0) cc_final: 0.7417 (mt0)
REVERT: B  505 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7592 (ttt)
REVERT: B  565 GLU cc_start: 0.7693 (mp0) cc_final: 0.7387 (mt-10)
REVERT: B  596 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6753 (tm-30)
REVERT: B  724 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7858 (m)
REVERT: B  728 LEU cc_start: 0.8124 (tp) cc_final: 0.7915 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 63
  average time/residue: 0.7776
  time to fit residues: 53.0831
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  505 MET
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 68 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0770
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3838 r_free = 0.3838 target = 0.157374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.115261 restraints weight = 6483.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.08
r_work: 0.3238 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5849  Z= 0.131
  Angle     :  0.522   8.087   7949  Z= 0.269
  Chirality :  0.040   0.123    868
  Planarity :  0.004   0.037   1015
  Dihedral  :  4.300  21.712    768
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.63 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.32), residues: 714
  helix:  1.72 (0.31), residues: 285
  sheet: -1.02 (0.73), residues: 50
  loop : -0.50 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 662 
 PHE   0.013   0.001   PHE B 668 
 TYR   0.017   0.001   TYR A 495 
 ARG   0.002   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  238)
  hydrogen bonds       : angle       4.18568 (  660)
  SS BOND              : bond        0.00205 (   21)
  SS BOND              : angle       0.77380 (   42)
  covalent geometry    : bond        0.00311 ( 5828)
  covalent geometry    : angle       0.52069 ( 7907)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  577 LYS cc_start: 0.7322 (ttpt) cc_final: 0.6838 (tppp)
REVERT: A  637 MET cc_start: 0.7730 (pmm) cc_final: 0.6960 (mmm)
REVERT: B  352 SER cc_start: 0.8709 (p) cc_final: 0.8327 (t)
REVERT: B  505 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7662 (ttt)
REVERT: B  565 GLU cc_start: 0.7676 (mp0) cc_final: 0.7366 (mt-10)
REVERT: B  596 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6729 (tm-30)
REVERT: B  724 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7859 (m)
REVERT: B  728 LEU cc_start: 0.8124 (tp) cc_final: 0.7919 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 63
  average time/residue: 0.7937
  time to fit residues: 54.1531
Evaluate side-chains
  63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  490 THR
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  505 MET
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  596 GLU
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  724 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 70 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0970
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3831 r_free = 0.3831 target = 0.156703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.114525 restraints weight = 6492.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.03
r_work: 0.3230 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5849  Z= 0.146
  Angle     :  0.531   8.073   7949  Z= 0.274
  Chirality :  0.041   0.131    868
  Planarity :  0.004   0.038   1015
  Dihedral  :  4.395  21.665    768
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.31 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.32), residues: 714
  helix:  1.67 (0.31), residues: 285
  sheet: -0.91 (0.79), residues: 46
  loop : -0.49 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 629 
 HIS   0.005   0.001   HIS B 662 
 PHE   0.014   0.001   PHE B 696 
 TYR   0.011   0.001   TYR A 495 
 ARG   0.003   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  238)
  hydrogen bonds       : angle       4.21261 (  660)
  SS BOND              : bond        0.00216 (   21)
  SS BOND              : angle       0.83203 (   42)
  covalent geometry    : bond        0.00349 ( 5828)
  covalent geometry    : angle       0.52877 ( 7907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4081.34 seconds
wall clock time: 71 minutes 38.92 seconds (4298.92 seconds total)