Starting phenix.real_space_refine
on Thu Jul  2 02:06:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8snn_40630/07_2026/8snn_40630.map"
  }
  resolution = 2.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.054
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
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0
          Ad-hoc single atom residues: {' CA': 1}
          Chain breaks: 1
  Time building chain proxies: 1.14, per 1000 atoms: 0.20
  Number of scatterers: 5685
  At special positions: 0
  Unit cell: (73.514, 85.078, 135.464, 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=2.03
    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=2.03
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS A 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 635 " distance=2.03
    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=2.03

  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: 0.38
  Conformation dependent library (CDL) restraints added in 197.6 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:
      24 helices and 7 sheets defined
      44.7% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 580 through 585
    Processing helix  chain 'A' and resid 595 through 599
      removed outlier: 3.843A  pdb=" N   SER A 599 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.873A  pdb=" N   GLN A 658 " --> pdb=" O   ASP A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 671
    Processing helix  chain 'A' and resid 671 through 703
      Proline residue:  A 686  - end of helix
    Processing helix  chain 'B' and resid 343 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 451 through 467
      removed outlier: 3.935A  pdb=" N   ASP B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
    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: 3.814A  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 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 637 through 660
      removed outlier: 5.013A  pdb=" N   ARG B 653 " --> pdb=" O   MET B 649 " (cutoff:3.500A)
      removed outlier: 3.747A  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 735
      removed outlier: 4.064A  pdb=" N   ALA B 719 " --> pdb=" O   ARG B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 759
      removed outlier: 3.530A  pdb=" N   PHE B 756 " --> pdb=" O   LEU B 752 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B 757 " --> pdb=" O   LEU B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 796
    Processing helix  chain 'B' and resid 802 through 809
    Processing sheet with id=AA1, first strand: chain 'A' and resid 533 through 535
    Processing sheet with id=AA2, first strand: chain 'A' and resid 572 through 574
    Processing sheet with id=AA3, first strand: chain 'A' and resid 589 through 591
      removed outlier: 3.725A  pdb=" N   GLU A 589 " --> pdb=" O   ARG A 605 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   CYS A 603 " --> pdb=" O   CYS A 591 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 612 " --> pdb=" O   CYS A 604 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 633 through 634
    Processing sheet with id=AA5, first strand: chain 'B' and resid 403 through 411
      removed outlier: 3.624A  pdb=" N   VAL B 410 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU B 418 " --> pdb=" O   VAL B 410 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 479 through 482
    Processing sheet with id=AA7, first strand: chain 'B' and resid 579 through 582

    248 hydrogen bonds defined for protein.
    711 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: 0.68

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1079
        1.33 -     1.45: 1496
        1.45 -     1.57: 3192
        1.57 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 5828
  Sorted by residual:
  bond pdb=" C   ILE A 672 "
       pdb=" O   ILE A 672 "
    ideal  model  delta    sigma   weight residual
    1.237  1.203  0.034 1.12e-02 7.97e+03 9.27e+00
  bond pdb=" C   VAL A 676 "
       pdb=" O   VAL A 676 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.13e-02 7.83e+03 6.02e+00
  bond pdb=" CA  TRP A 684 "
       pdb=" C   TRP A 684 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.24e-02 6.50e+03 4.72e+00
  bond pdb=" CA  ALA B 518 "
       pdb=" C   ALA B 518 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.34e-02 5.57e+03 4.45e+00
  bond pdb=" C   TRP A 684 "
       pdb=" O   TRP A 684 "
    ideal  model  delta    sigma   weight residual
    1.236  1.214  0.023 1.15e-02 7.56e+03 3.92e+00
  ... (remaining 5823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 7637
        1.56 -     3.11: 222
        3.11 -     4.67: 34
        4.67 -     6.22: 11
        6.22 -     7.78: 3
  Bond angle restraints: 7907
  Sorted by residual:
  angle pdb=" N   GLU A 488 "
        pdb=" CA  GLU A 488 "
        pdb=" C   GLU A 488 "
      ideal   model   delta    sigma   weight residual
     111.28  106.05    5.23 1.09e+00 8.42e-01 2.30e+01
  angle pdb=" N   ASP A 699 "
        pdb=" CA  ASP A 699 "
        pdb=" C   ASP A 699 "
      ideal   model   delta    sigma   weight residual
     111.28  116.26   -4.98 1.09e+00 8.42e-01 2.09e+01
  angle pdb=" N   ALA B 518 "
        pdb=" CA  ALA B 518 "
        pdb=" C   ALA B 518 "
      ideal   model   delta    sigma   weight residual
     110.80  103.02    7.78 2.13e+00 2.20e-01 1.33e+01
  angle pdb=" O   PRO B 503 "
        pdb=" C   PRO B 503 "
        pdb=" N   PRO B 504 "
      ideal   model   delta    sigma   weight residual
     121.15  122.79   -1.64 4.70e-01 4.53e+00 1.21e+01
  angle pdb=" N   SER B 516 "
        pdb=" CA  SER B 516 "
        pdb=" C   SER B 516 "
      ideal   model   delta    sigma   weight residual
     107.75  113.89   -6.14 1.86e+00 2.89e-01 1.09e+01
  ... (remaining 7902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.77: 3123
       15.77 -    31.54: 309
       31.54 -    47.31: 50
       47.31 -    63.08: 12
       63.08 -    78.85: 11
  Dihedral angle restraints: 3505
    sinusoidal: 1429
      harmonic: 2076
  Sorted by residual:
  dihedral pdb=" CB  CYS A 567 "
           pdb=" SG  CYS A 567 "
           pdb=" SG  CYS A 578 "
           pdb=" CB  CYS A 578 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.76  -48.76     1      1.00e+01 1.00e-02 3.27e+01
  dihedral pdb=" CB  CYS A 501 "
           pdb=" SG  CYS A 501 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.74   43.74     1      1.00e+01 1.00e-02 2.66e+01
  dihedral pdb=" CA  PHE B 428 "
           pdb=" C   PHE B 428 "
           pdb=" N   TRP B 429 "
           pdb=" CA  TRP B 429 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.95   21.05     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 3502 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 791
       0.071 -    0.143: 73
       0.143 -    0.214: 3
       0.214 -    0.286: 0
       0.286 -    0.357: 1
  Chirality restraints: 868
  Sorted by residual:
  chirality pdb=" CA  ASP A 699 "
            pdb=" N   ASP A 699 "
            pdb=" C   ASP A 699 "
            pdb=" CB  ASP A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CG  LEU B 600 "
            pdb=" CB  LEU B 600 "
            pdb=" CD1 LEU B 600 "
            pdb=" CD2 LEU B 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.58e-01
  chirality pdb=" CA  LEU A 698 "
            pdb=" N   LEU A 698 "
            pdb=" C   LEU A 698 "
            pdb=" CB  LEU A 698 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.22e-01
  ... (remaining 865 not shown)

  Planarity restraints: 1015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 797 "   -0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO B 798 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 798 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 798 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 700 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   LYS A 700 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   LYS A 700 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLN A 701 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 554 "    0.006 2.00e-02 2.50e+03   1.31e-02 1.73e+00
        pdb=" C   SER B 554 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   SER B 554 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN B 555 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1012 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 625
        2.75 -     3.28: 5766
        3.28 -     3.82: 10012
        3.82 -     4.36: 11980
        4.36 -     4.90: 19643
  Nonbonded interactions: 48026
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 450 "
            pdb=" O   GLU B 620 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   PHE B 668 "
            pdb=" OG  SER B 694 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" NH2 ARG A 651 "
            pdb=" O   PRO B 615 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" NH1 ARG B 355 "
            pdb=" OG  SER B 356 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD2 ASP A 569 "
            pdb=" OG  SER B 533 "
     model   vdw
     2.270 3.040
  ... (remaining 48021 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:             3.570
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.960
  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:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
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      :  0.003   0.041   5849  Z= 0.215
  Angle     :  0.644   7.778   7949  Z= 0.379
  Chirality :  0.043   0.357    868
  Planarity :  0.003   0.040   1015
  Dihedral  : 13.117  78.846   2102
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.31), residues: 714
  helix:  1.22 (0.31), residues: 285
  sheet: -0.96 (0.85), residues: 36
  loop : -0.78 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 355 
 TYR   0.006   0.001   TYR B 820 
 PHE   0.012   0.001   PHE B 668 
 TRP   0.012   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.22 ( 5828)
  covalent geometry    : angle       0.64137 /  0.38 ( 7907)
  SS BOND              : bond        0.00189 /  0.14 (   21)
  SS BOND              : angle       1.03518 /  0.83 (   42)
  hydrogen bonds       : bond        0.15671 / 10.26 (  248)
  hydrogen bonds       : angle       6.90586 /  4.66 (  711)

*********************** 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
  129 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  614 TYR cc_start: 0.7997 (t80) cc_final: 0.7674 (t80)
REVERT: A  616 ASP cc_start: 0.6141 (t0) cc_final: 0.5902 (t0)
REVERT: A  647 ASP cc_start: 0.6161 (t0) cc_final: 0.5777 (m-30)
REVERT: B  590 MET cc_start: 0.9060 (mmm) cc_final: 0.8836 (mmm)
REVERT: B  749 LEU cc_start: 0.8544 (mt) cc_final: 0.8292 (tp)
  outliers start: 0
  outliers final: 1
  residues processed: 129
  average time/residue: 0.4575
  time to fit residues: 61.5795
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 621 ASN
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 ASN
B 427 ASN
** B 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.154989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116250 restraints weight = 5828.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.61
r_work: 0.3301 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5849  Z= 0.146
  Angle     :  0.589   6.711   7949  Z= 0.311
  Chirality :  0.042   0.157    868
  Planarity :  0.004   0.044   1015
  Dihedral  :  5.097  56.353    770
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.67 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.26 (0.30), residues: 714
  helix:  1.40 (0.30), residues: 285
  sheet: -1.04 (0.86), residues: 36
  loop : -0.62 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 610 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.011   0.001   TRP B 710 
 HIS   0.003   0.001   HIS B 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 5828)
  covalent geometry    : angle       0.58298 /  0.31 ( 7907)
  SS BOND              : bond        0.00203 /  0.13 (   21)
  SS BOND              : angle       1.25225 /  0.99 (   42)
  hydrogen bonds       : bond        0.04537 /  2.92 (  248)
  hydrogen bonds       : angle       5.29165 /  3.69 (  711)

*********************** 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
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 ASP cc_start: 0.6537 (t0) cc_final: 0.6286 (t0)
REVERT: A  643 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8419 (mtpp)
REVERT: A  672 ILE cc_start: 0.9036 (mt) cc_final: 0.8788 (tp)
REVERT: A  697 LYS cc_start: 0.7513 (tttt) cc_final: 0.6556 (mptm)
REVERT: B  567 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7847 (mptm)
REVERT: B  749 LEU cc_start: 0.8940 (mt) cc_final: 0.8661 (tp)
REVERT: B  770 TYR cc_start: 0.8445 (m-10) cc_final: 0.8164 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.5111
  time to fit residues: 44.9611
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0270
   chunk 22 optimal weight:    0.0670
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.3776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 648 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.155419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.116840 restraints weight = 5714.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.59
r_work: 0.3308 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5849  Z= 0.123
  Angle     :  0.560   9.003   7949  Z= 0.294
  Chirality :  0.041   0.257    868
  Planarity :  0.004   0.043   1015
  Dihedral  :  4.992  54.191    770
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.73 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.28 (0.31), residues: 714
  helix:  1.42 (0.30), residues: 295
  sheet: -0.91 (0.90), residues: 36
  loop : -0.68 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 610 
 TYR   0.011   0.001   TYR B 340 
 PHE   0.015   0.001   PHE B 668 
 TRP   0.011   0.001   TRP B 429 
 HIS   0.002   0.001   HIS B 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 5828)
  covalent geometry    : angle       0.55017 /  0.29 ( 7907)
  SS BOND              : bond        0.00477 /  0.21 (   21)
  SS BOND              : angle       1.53452 /  0.96 (   42)
  hydrogen bonds       : bond        0.04075 /  2.63 (  248)
  hydrogen bonds       : angle       5.02554 /  3.50 (  711)

*********************** 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
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 SER cc_start: 0.8659 (p) cc_final: 0.8284 (m)
REVERT: A  577 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7745 (tppt)
REVERT: A  672 ILE cc_start: 0.9028 (mt) cc_final: 0.8799 (tp)
REVERT: B  455 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8145 (mt-10)
REVERT: B  749 LEU cc_start: 0.8928 (mt) cc_final: 0.8647 (tp)
REVERT: B  770 TYR cc_start: 0.8420 (m-10) cc_final: 0.8156 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 76
  average time/residue: 0.5507
  time to fit residues: 43.6780
Evaluate side-chains
  69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0370
   chunk 60 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 722 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.154165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.115429 restraints weight = 5674.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.59
r_work: 0.3286 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5849  Z= 0.130
  Angle     :  0.554   9.453   7949  Z= 0.290
  Chirality :  0.042   0.219    868
  Planarity :  0.004   0.047   1015
  Dihedral  :  4.626  22.473    768
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.31), residues: 714
  helix:  1.45 (0.30), residues: 295
  sheet: -0.92 (0.92), residues: 36
  loop : -0.64 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 610 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.015   0.001   PHE B 668 
 TRP   0.010   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 5828)
  covalent geometry    : angle       0.54759 /  0.29 ( 7907)
  SS BOND              : bond        0.00200 /  0.13 (   21)
  SS BOND              : angle       1.30591 /  0.85 (   42)
  hydrogen bonds       : bond        0.04134 /  2.66 (  248)
  hydrogen bonds       : angle       4.96657 /  3.46 (  711)

*********************** 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
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8623 (p) cc_final: 0.8281 (m)
REVERT: A  505 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6921 (p0)
REVERT: A  577 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7739 (tppt)
REVERT: A  647 ASP cc_start: 0.6756 (t0) cc_final: 0.6500 (t0)
REVERT: A  672 ILE cc_start: 0.9040 (mt) cc_final: 0.8816 (tp)
REVERT: B  414 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7475 (mttp)
REVERT: B  455 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8194 (mt-10)
REVERT: B  749 LEU cc_start: 0.8948 (mt) cc_final: 0.8689 (tp)
REVERT: B  770 TYR cc_start: 0.8411 (m-10) cc_final: 0.8146 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 76
  average time/residue: 0.5364
  time to fit residues: 42.6108
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  414 LYS
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0870
   chunk 52 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 648 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.152829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.113882 restraints weight = 5840.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.60
r_work: 0.3264 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5849  Z= 0.141
  Angle     :  0.568   9.226   7949  Z= 0.298
  Chirality :  0.042   0.193    868
  Planarity :  0.004   0.053   1015
  Dihedral  :  4.729  22.703    768
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.15 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.30 (0.31), residues: 714
  helix:  1.40 (0.30), residues: 295
  sheet: -1.28 (0.78), residues: 45
  loop : -0.56 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 610 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.015   0.001   PHE B 668 
 TRP   0.010   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 5828)
  covalent geometry    : angle       0.56230 /  0.30 ( 7907)
  SS BOND              : bond        0.00197 /  0.14 (   21)
  SS BOND              : angle       1.26891 /  0.85 (   42)
  hydrogen bonds       : bond        0.04283 /  2.75 (  248)
  hydrogen bonds       : angle       4.96988 /  3.47 (  711)

*********************** 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
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8662 (p) cc_final: 0.8325 (m)
REVERT: A  505 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7013 (p0)
REVERT: A  595 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6704 (pm20)
REVERT: A  647 ASP cc_start: 0.6769 (t0) cc_final: 0.6542 (t0)
REVERT: A  672 ILE cc_start: 0.9037 (mt) cc_final: 0.8822 (tp)
REVERT: B  354 ARG cc_start: 0.7573 (mtp180) cc_final: 0.7171 (mtm110)
REVERT: B  414 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7523 (mttp)
REVERT: B  489 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6850 (mp0)
REVERT: B  749 LEU cc_start: 0.8955 (mt) cc_final: 0.8697 (tp)
REVERT: B  770 TYR cc_start: 0.8438 (m-10) cc_final: 0.8168 (m-10)
  outliers start: 18
  outliers final: 12
  residues processed: 82
  average time/residue: 0.5066
  time to fit residues: 43.3229
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  414 LYS
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0050
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.4794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 648 GLN ** 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 = 0.3877 r_free = 0.3877 target = 0.153772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.115048 restraints weight = 5740.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.59
r_work: 0.3278 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5849  Z= 0.127
  Angle     :  0.547   8.801   7949  Z= 0.287
  Chirality :  0.041   0.184    868
  Planarity :  0.004   0.064   1015
  Dihedral  :  4.682  22.708    768
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.10 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.35 (0.31), residues: 714
  helix:  1.46 (0.30), residues: 295
  sheet: -0.99 (0.93), residues: 36
  loop : -0.61 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 610 
 TYR   0.011   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 668 
 TRP   0.011   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 5828)
  covalent geometry    : angle       0.54143 /  0.29 ( 7907)
  SS BOND              : bond        0.00175 /  0.12 (   21)
  SS BOND              : angle       1.21579 /  0.84 (   42)
  hydrogen bonds       : bond        0.04030 /  2.60 (  248)
  hydrogen bonds       : angle       4.88616 /  3.41 (  711)

*********************** 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
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8698 (p) cc_final: 0.8494 (m)
REVERT: A  595 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6706 (pm20)
REVERT: A  647 ASP cc_start: 0.6826 (t0) cc_final: 0.6601 (t0)
REVERT: A  672 ILE cc_start: 0.9036 (mt) cc_final: 0.8825 (tp)
REVERT: B  354 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7179 (mtm110)
REVERT: B  414 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7482 (mttp)
REVERT: B  489 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6852 (mp0)
REVERT: B  749 LEU cc_start: 0.8952 (mt) cc_final: 0.8696 (tp)
REVERT: B  769 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7818 (ptmm)
REVERT: B  770 TYR cc_start: 0.8442 (m-10) cc_final: 0.8181 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 81
  average time/residue: 0.6057
  time to fit residues: 51.3169
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  637 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LYS
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 364 GLN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 GLN
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.151178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112303 restraints weight = 5727.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.58
r_work: 0.3236 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5849  Z= 0.165
  Angle     :  0.600   8.824   7949  Z= 0.314
  Chirality :  0.043   0.184    868
  Planarity :  0.004   0.072   1015
  Dihedral  :  4.903  22.900    768
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.95 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.23 (0.31), residues: 714
  helix:  1.33 (0.30), residues: 295
  sheet: -1.40 (0.83), residues: 41
  loop : -0.59 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 610 
 TYR   0.015   0.002   TYR B 340 
 PHE   0.014   0.002   PHE B 668 
 TRP   0.010   0.002   TRP B 710 
 HIS   0.004   0.001   HIS B 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 5828)
  covalent geometry    : angle       0.59338 /  0.31 ( 7907)
  SS BOND              : bond        0.00219 /  0.16 (   21)
  SS BOND              : angle       1.34944 /  0.92 (   42)
  hydrogen bonds       : bond        0.04578 /  2.93 (  248)
  hydrogen bonds       : angle       5.02836 /  3.51 (  711)

*********************** 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
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7221 (p0)
REVERT: A  595 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6750 (pm20)
REVERT: A  672 ILE cc_start: 0.9019 (mt) cc_final: 0.8810 (tp)
REVERT: B  354 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7220 (mtm110)
REVERT: B  414 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7555 (mttp)
REVERT: B  769 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7798 (ptmm)
REVERT: B  770 TYR cc_start: 0.8396 (m-10) cc_final: 0.8129 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 81
  average time/residue: 0.5949
  time to fit residues: 50.4096
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  567 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LYS
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 GLN
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.153204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.114681 restraints weight = 5741.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.59
r_work: 0.3275 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5849  Z= 0.121
  Angle     :  0.550   8.782   7949  Z= 0.288
  Chirality :  0.041   0.177    868
  Planarity :  0.004   0.084   1015
  Dihedral  :  4.698  22.791    768
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.58 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.34 (0.31), residues: 714
  helix:  1.48 (0.30), residues: 295
  sheet: -0.97 (0.85), residues: 40
  loop : -0.64 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 610 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 668 
 TRP   0.013   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 5828)
  covalent geometry    : angle       0.54388 /  0.29 ( 7907)
  SS BOND              : bond        0.00166 /  0.12 (   21)
  SS BOND              : angle       1.22348 /  0.84 (   42)
  hydrogen bonds       : bond        0.03961 /  2.55 (  248)
  hydrogen bonds       : angle       4.87509 /  3.41 (  711)

*********************** 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
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7342 (p0)
REVERT: A  595 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6831 (pm20)
REVERT: A  610 ARG cc_start: 0.7902 (ttm110) cc_final: 0.6933 (tpt90)
REVERT: A  651 ARG cc_start: 0.8354 (mmm160) cc_final: 0.7967 (mtm180)
REVERT: B  354 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7204 (mtm110)
REVERT: B  363 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7357 (ptp-170)
REVERT: B  489 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6894 (mp0)
REVERT: B  749 LEU cc_start: 0.8949 (mt) cc_final: 0.8700 (tp)
REVERT: B  769 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7776 (ptmm)
REVERT: B  770 TYR cc_start: 0.8366 (m-10) cc_final: 0.8099 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 78
  average time/residue: 0.6115
  time to fit residues: 49.9445
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 GLN
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.151882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113222 restraints weight = 5759.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.59
r_work: 0.3249 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5849  Z= 0.144
  Angle     :  0.574   8.752   7949  Z= 0.301
  Chirality :  0.042   0.177    868
  Planarity :  0.004   0.073   1015
  Dihedral  :  4.781  22.660    768
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.06 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.25 (0.30), residues: 714
  helix:  1.39 (0.30), residues: 295
  sheet: -1.42 (0.84), residues: 41
  loop : -0.62 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 610 
 TYR   0.013   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 668 
 TRP   0.011   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 5828)
  covalent geometry    : angle       0.56740 /  0.30 ( 7907)
  SS BOND              : bond        0.00186 /  0.14 (   21)
  SS BOND              : angle       1.31116 /  0.90 (   42)
  hydrogen bonds       : bond        0.04289 /  2.76 (  248)
  hydrogen bonds       : angle       4.94148 /  3.45 (  711)

*********************** 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
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7059 (t70) cc_final: 0.6452 (t70)
REVERT: A  595 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6830 (pm20)
REVERT: A  610 ARG cc_start: 0.7908 (ttm110) cc_final: 0.6982 (tpt90)
REVERT: B  354 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7205 (mtm110)
REVERT: B  363 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7380 (ptp-170)
REVERT: B  749 LEU cc_start: 0.8971 (mt) cc_final: 0.8713 (tp)
REVERT: B  769 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7756 (ptmm)
REVERT: B  770 TYR cc_start: 0.8380 (m-10) cc_final: 0.8111 (m-10)
REVERT: B  773 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8396 (mtt180)
  outliers start: 19
  outliers final: 13
  residues processed: 80
  average time/residue: 0.6084
  time to fit residues: 50.8691
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  582 THR
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0020
   chunk 48 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 36 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.2788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 GLN
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.154486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.116216 restraints weight = 5831.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.60
r_work: 0.3296 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5849  Z= 0.108
  Angle     :  0.534   8.744   7949  Z= 0.280
  Chirality :  0.040   0.170    868
  Planarity :  0.004   0.071   1015
  Dihedral  :  4.580  22.759    768
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.53 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.37 (0.31), residues: 714
  helix:  1.54 (0.30), residues: 295
  sheet: -0.89 (0.85), residues: 40
  loop : -0.66 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 610 
 TYR   0.011   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 668 
 TRP   0.014   0.001   TRP B 429 
 HIS   0.002   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 ( 5828)
  covalent geometry    : angle       0.52817 /  0.28 ( 7907)
  SS BOND              : bond        0.00161 /  0.11 (   21)
  SS BOND              : angle       1.19554 /  0.83 (   42)
  hydrogen bonds       : bond        0.03720 /  2.40 (  248)
  hydrogen bonds       : angle       4.78235 /  3.34 (  711)

********************** 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
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.6974 (t70) cc_final: 0.6359 (t70)
REVERT: A  595 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6802 (pm20)
REVERT: A  610 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7015 (tpt90)
REVERT: B  363 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7403 (ptp-170)
REVERT: B  749 LEU cc_start: 0.8955 (mt) cc_final: 0.8704 (tp)
REVERT: B  769 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7728 (ptmm)
REVERT: B  770 TYR cc_start: 0.8369 (m-10) cc_final: 0.8103 (m-10)
REVERT: B  773 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8326 (mtt180)
  outliers start: 15
  outliers final: 11
  residues processed: 77
  average time/residue: 0.5225
  time to fit residues: 42.1035
Evaluate side-chains
  75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 347 ASN
B 595 HIS
** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.150161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111335 restraints weight = 5646.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.57
r_work: 0.3223 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5849  Z= 0.197
  Angle     :  0.633   8.757   7949  Z= 0.332
  Chirality :  0.045   0.179    868
  Planarity :  0.004   0.066   1015
  Dihedral  :  4.983  22.408    768
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.01 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  0.16 (0.30), residues: 714
  helix:  1.28 (0.30), residues: 295
  sheet: -1.29 (0.83), residues: 41
  loop : -0.65 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 610 
 TYR   0.014   0.002   TYR B 340 
 PHE   0.016   0.002   PHE B 783 
 TRP   0.010   0.002   TRP B 710 
 HIS   0.005   0.001   HIS B 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.20 ( 5828)
  covalent geometry    : angle       0.62502 /  0.33 ( 7907)
  SS BOND              : bond        0.00252 /  0.18 (   21)
  SS BOND              : angle       1.48539 /  1.04 (   42)
  hydrogen bonds       : bond        0.04868 /  3.10 (  248)
  hydrogen bonds       : angle       5.07140 /  3.54 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2615.93 seconds
wall clock time: 45 minutes 14.45 seconds (2714.45 seconds total)