Starting phenix.real_space_refine
on Fri Aug 22 16:14:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8snn_40630/08_2025/8snn_40630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8snn_40630/08_2025/8snn_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_40630/08_2025/8snn_40630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8snn_40630/08_2025/8snn_40630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8snn_40630/08_2025/8snn_40630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8snn_40630/08_2025/8snn_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-2.0-5787/lib/python3.9/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, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.24
  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: 0.51
  Conformation dependent library (CDL) restraints added in 260.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.15
  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: 0.90

  Time building geometry restraints manager: 0.70 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:             5.370
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.430
  Find NCS groups from input model:        0.020
  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:8.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
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 aren 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
  covalent geometry    : bond        0.00337 ( 5828)
  covalent geometry    : angle       0.64137 ( 7907)
  SS BOND              : bond        0.00189 (   21)
  SS BOND              : angle       1.03518 (   42)
  hydrogen bonds       : bond        0.15671 (  248)
  hydrogen bonds       : angle       6.90586 (  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  : 0.253 
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: 0.6194
  time to fit residues: 83.2401
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  : 0.230 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3887 r_free = 0.3887 target = 0.154723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116421 restraints weight = 5887.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.60
r_work: 0.3303 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2012

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= 0.143
  Angle     :  0.585   6.653   7949  Z= 0.309
  Chirality :  0.042   0.163    868
  Planarity :  0.004   0.046   1015
  Dihedral  :  5.086  56.944    770
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.83 %
    Favored  : 88.11 %
  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 aren not related in a simple way.
  whole:  0.26 (0.30), residues: 714
  helix:  1.41 (0.30), residues: 285
  sheet: -1.02 (0.86), residues: 36
  loop : -0.64 (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 429 
 HIS   0.003   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5828)
  covalent geometry    : angle       0.57957 ( 7907)
  SS BOND              : bond        0.00321 (   21)
  SS BOND              : angle       1.21041 (   42)
  hydrogen bonds       : bond        0.04532 (  248)
  hydrogen bonds       : angle       5.29505 (  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  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 ASP cc_start: 0.6540 (t0) cc_final: 0.6287 (t0)
REVERT: A  643 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8417 (mtpp)
REVERT: A  672 ILE cc_start: 0.9037 (mt) cc_final: 0.8782 (tp)
REVERT: A  697 LYS cc_start: 0.7514 (tttt) cc_final: 0.6545 (mptm)
REVERT: B  567 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7851 (mptm)
REVERT: B  749 LEU cc_start: 0.8947 (mt) cc_final: 0.8662 (tp)
REVERT: B  770 TYR cc_start: 0.8428 (m-10) cc_final: 0.8143 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.6247
  time to fit residues: 54.7474
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  : 0.205 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0070
   chunk 22 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 635 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.152118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113422 restraints weight = 5693.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.57
r_work: 0.3257 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5849  Z= 0.166
  Angle     :  0.610   7.797   7949  Z= 0.320
  Chirality :  0.043   0.241    868
  Planarity :  0.004   0.042   1015
  Dihedral  :  5.233  53.890    770
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.20 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.30), residues: 714
  helix:  1.35 (0.30), residues: 287
  sheet: -0.83 (0.90), residues: 36
  loop : -0.68 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 610 
 TYR   0.014   0.002   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.010   0.002   TRP B 429 
 HIS   0.004   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 5828)
  covalent geometry    : angle       0.60055 ( 7907)
  SS BOND              : bond        0.00307 (   21)
  SS BOND              : angle       1.57752 (   42)
  hydrogen bonds       : bond        0.04698 (  248)
  hydrogen bonds       : angle       5.18254 (  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
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 SER cc_start: 0.8671 (p) cc_final: 0.8287 (m)
REVERT: A  672 ILE cc_start: 0.9052 (mt) cc_final: 0.8811 (tp)
REVERT: B  354 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7111 (mtm110)
REVERT: B  567 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7965 (mptm)
REVERT: B  749 LEU cc_start: 0.8962 (mt) cc_final: 0.8695 (tp)
REVERT: B  770 TYR cc_start: 0.8434 (m-10) cc_final: 0.8173 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 79
  average time/residue: 0.6585
  time to fit residues: 54.2459
Evaluate side-chains
  74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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  648 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  419 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 364 GLN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 ASN
** 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 = 0.3845 r_free = 0.3845 target = 0.151372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112707 restraints weight = 5688.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.57
r_work: 0.3246 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5849  Z= 0.160
  Angle     :  0.595  10.303   7949  Z= 0.312
  Chirality :  0.043   0.223    868
  Planarity :  0.004   0.049   1015
  Dihedral  :  4.883  22.795    768
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.47 %
    Favored  : 84.15 %
  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 aren not related in a simple way.
  whole:  0.23 (0.31), residues: 714
  helix:  1.30 (0.30), residues: 295
  sheet: -0.84 (0.92), residues: 36
  loop : -0.65 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 610 
 TYR   0.013   0.002   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.011   0.002   TRP B 429 
 HIS   0.004   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5828)
  covalent geometry    : angle       0.58766 ( 7907)
  SS BOND              : bond        0.00223 (   21)
  SS BOND              : angle       1.40801 (   42)
  hydrogen bonds       : bond        0.04554 (  248)
  hydrogen bonds       : angle       5.11302 (  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
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 SER cc_start: 0.8712 (p) cc_final: 0.8371 (m)
REVERT: A  505 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7048 (p0)
REVERT: A  595 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6721 (pm20)
REVERT: A  647 ASP cc_start: 0.6860 (t0) cc_final: 0.6571 (t0)
REVERT: A  672 ILE cc_start: 0.9049 (mt) cc_final: 0.8833 (tp)
REVERT: B  354 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7176 (mtm110)
REVERT: B  414 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7526 (mttp)
REVERT: B  567 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7979 (mptm)
REVERT: B  749 LEU cc_start: 0.8964 (mt) cc_final: 0.8718 (tp)
REVERT: B  770 TYR cc_start: 0.8426 (m-10) cc_final: 0.8166 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 83
  average time/residue: 0.7305
  time to fit residues: 63.0525
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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  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  411 LEU
Chi-restraints excluded: chain B residue  414 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:    0.0370
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 63 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3860 r_free = 0.3860 target = 0.152654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.114134 restraints weight = 5890.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.61
r_work: 0.3267 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5849  Z= 0.131
  Angle     :  0.555   9.442   7949  Z= 0.292
  Chirality :  0.042   0.187    868
  Planarity :  0.004   0.054   1015
  Dihedral  :  4.749  22.587    768
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.63 %
    Favored  : 83.52 %
  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 aren not related in a simple way.
  whole:  0.27 (0.31), residues: 714
  helix:  1.44 (0.30), residues: 295
  sheet: -0.88 (0.86), residues: 40
  loop : -0.70 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 610 
 TYR   0.010   0.001   TYR B 340 
 PHE   0.015   0.001   PHE B 668 
 TRP   0.012   0.001   TRP B 429 
 HIS   0.005   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5828)
  covalent geometry    : angle       0.54872 ( 7907)
  SS BOND              : bond        0.00202 (   21)
  SS BOND              : angle       1.26833 (   42)
  hydrogen bonds       : bond        0.04138 (  248)
  hydrogen bonds       : angle       4.97461 (  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  : 0.256 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8746 (p) cc_final: 0.8540 (m)
REVERT: A  505 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7196 (p0)
REVERT: A  584 ARG cc_start: 0.7870 (ptt90) cc_final: 0.7640 (ttp-110)
REVERT: A  595 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6710 (pm20)
REVERT: A  647 ASP cc_start: 0.6832 (t0) cc_final: 0.6551 (t0)
REVERT: A  672 ILE cc_start: 0.9031 (mt) cc_final: 0.8826 (tp)
REVERT: B  354 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7159 (mtm110)
REVERT: B  414 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7474 (mttp)
REVERT: B  489 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6895 (mp0)
REVERT: B  567 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7885 (mptm)
REVERT: B  749 LEU cc_start: 0.8958 (mt) cc_final: 0.8707 (tp)
REVERT: B  769 LYS cc_start: 0.8254 (ptmt) cc_final: 0.8041 (ptmm)
REVERT: B  770 TYR cc_start: 0.8428 (m-10) cc_final: 0.8158 (m-10)
  outliers start: 18
  outliers final: 10
  residues processed: 83
  average time/residue: 0.7130
  time to fit residues: 61.5709
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  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  406 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LYS
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  567 LYS
Chi-restraints excluded: chain B residue  689 VAL
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:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS
** 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 = 0.3845 r_free = 0.3845 target = 0.151431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112754 restraints weight = 5747.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.59
r_work: 0.3243 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5849  Z= 0.150
  Angle     :  0.577   8.826   7949  Z= 0.304
  Chirality :  0.042   0.185    868
  Planarity :  0.004   0.064   1015
  Dihedral  :  4.839  22.713    768
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.95 %
    Favored  : 83.04 %
  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 aren not related in a simple way.
  whole:  0.22 (0.31), residues: 714
  helix:  1.38 (0.30), residues: 295
  sheet: -1.36 (0.78), residues: 45
  loop : -0.64 (0.30), residues: 374

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   0.015   0.002   PHE B 668 
 TRP   0.010   0.001   TRP B 429 
 HIS   0.005   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5828)
  covalent geometry    : angle       0.57125 ( 7907)
  SS BOND              : bond        0.00203 (   21)
  SS BOND              : angle       1.28447 (   42)
  hydrogen bonds       : bond        0.04397 (  248)
  hydrogen bonds       : angle       5.00298 (  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
  89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (p0)
REVERT: A  595 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6758 (pm20)
REVERT: A  647 ASP cc_start: 0.6897 (t0) cc_final: 0.6626 (t0)
REVERT: A  672 ILE cc_start: 0.9040 (mt) cc_final: 0.8828 (tp)
REVERT: B  354 ARG cc_start: 0.7604 (mtp180) cc_final: 0.7214 (mtm110)
REVERT: B  414 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7514 (mttp)
REVERT: B  567 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7922 (mptm)
REVERT: B  749 LEU cc_start: 0.8968 (mt) cc_final: 0.8709 (tp)
REVERT: B  770 TYR cc_start: 0.8438 (m-10) cc_final: 0.8176 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 83
  average time/residue: 0.7026
  time to fit residues: 60.7084
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  414 LYS
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0570
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3835 r_free = 0.3835 target = 0.150531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111976 restraints weight = 5776.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.59
r_work: 0.3235 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5849  Z= 0.161
  Angle     :  0.592   8.813   7949  Z= 0.312
  Chirality :  0.043   0.184    868
  Planarity :  0.004   0.070   1015
  Dihedral  :  4.911  22.684    768
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.79 %
    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 aren not related in a simple way.
  whole:  0.17 (0.30), residues: 714
  helix:  1.33 (0.30), residues: 295
  sheet: -1.41 (0.84), residues: 41
  loop : -0.67 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 610 
 TYR   0.013   0.002   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.011   0.002   TRP B 429 
 HIS   0.004   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5828)
  covalent geometry    : angle       0.58534 ( 7907)
  SS BOND              : bond        0.00207 (   21)
  SS BOND              : angle       1.34731 (   42)
  hydrogen bonds       : bond        0.04522 (  248)
  hydrogen bonds       : angle       5.02313 (  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
  87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7359 (p0)
REVERT: A  595 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6763 (pm20)
REVERT: A  647 ASP cc_start: 0.6876 (t0) cc_final: 0.6662 (t0)
REVERT: B  354 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7217 (mtm110)
REVERT: B  363 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7390 (ptp-170)
REVERT: B  414 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7506 (mttp)
REVERT: B  489 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6904 (mp0)
REVERT: B  567 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7951 (mptm)
REVERT: B  769 LYS cc_start: 0.8288 (ptmt) cc_final: 0.8078 (ptmm)
REVERT: B  770 TYR cc_start: 0.8410 (m-10) cc_final: 0.8147 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 81
  average time/residue: 0.7100
  time to fit residues: 59.7734
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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 B residue  342 LEU
Chi-restraints excluded: chain B residue  363 ARG
Chi-restraints excluded: chain B residue  369 ASP
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  419 SER
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3840 r_free = 0.3840 target = 0.150998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112522 restraints weight = 5749.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.58
r_work: 0.3243 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5849  Z= 0.149
  Angle     :  0.579   8.748   7949  Z= 0.306
  Chirality :  0.042   0.179    868
  Planarity :  0.004   0.081   1015
  Dihedral  :  4.860  22.739    768
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.26 %
    Favored  : 82.41 %
  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 aren not related in a simple way.
  whole:  0.23 (0.31), residues: 714
  helix:  1.38 (0.30), residues: 295
  sheet: -1.34 (0.78), residues: 45
  loop : -0.63 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 610 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 668 
 TRP   0.012   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5828)
  covalent geometry    : angle       0.57277 ( 7907)
  SS BOND              : bond        0.00198 (   21)
  SS BOND              : angle       1.33792 (   42)
  hydrogen bonds       : bond        0.04380 (  248)
  hydrogen bonds       : angle       4.98153 (  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
  87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  595 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6803 (pm20)
REVERT: A  610 ARG cc_start: 0.7918 (ttm110) cc_final: 0.6998 (tpt90)
REVERT: B  354 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7221 (mtm110)
REVERT: B  363 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7377 (ptp-170)
REVERT: B  414 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7490 (mttp)
REVERT: B  489 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6902 (mp0)
REVERT: B  567 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7928 (mptm)
REVERT: B  715 ARG cc_start: 0.7382 (tpt-90) cc_final: 0.7108 (tpm170)
REVERT: B  769 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7809 (ptmm)
REVERT: B  770 TYR cc_start: 0.8390 (m-10) cc_final: 0.8130 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 82
  average time/residue: 0.7165
  time to fit residues: 61.0737
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  : 0.218 
-------------------------------------------------------------------------------
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  567 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  369 ASP
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  419 SER
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3833 r_free = 0.3833 target = 0.150297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111712 restraints weight = 5760.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.58
r_work: 0.3232 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.3191

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= 0.160
  Angle     :  0.597   8.915   7949  Z= 0.314
  Chirality :  0.043   0.179    868
  Planarity :  0.004   0.073   1015
  Dihedral  :  4.928  22.682    768
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.06 %
    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 aren not related in a simple way.
  whole:  0.18 (0.30), residues: 714
  helix:  1.32 (0.30), residues: 296
  sheet: -1.32 (0.78), residues: 45
  loop : -0.66 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 610 
 TYR   0.013   0.001   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.011   0.002   TRP B 429 
 HIS   0.004   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5828)
  covalent geometry    : angle       0.59076 ( 7907)
  SS BOND              : bond        0.00206 (   21)
  SS BOND              : angle       1.36450 (   42)
  hydrogen bonds       : bond        0.04544 (  248)
  hydrogen bonds       : angle       5.01247 (  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: 20
    poor density    : 64
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7306 (t70) cc_final: 0.6597 (t70)
REVERT: B  354 ARG cc_start: 0.7607 (mtp180) cc_final: 0.7247 (mtm110)
REVERT: B  363 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7400 (ptp-170)
REVERT: B  414 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7522 (mttp)
REVERT: B  489 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6928 (mp0)
REVERT: B  567 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8007 (mptm)
REVERT: B  715 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.7148 (tpm170)
REVERT: B  770 TYR cc_start: 0.8397 (m-10) cc_final: 0.8132 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 78
  average time/residue: 0.7111
  time to fit residues: 57.5838
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  567 CYS
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  369 ASP
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  419 SER
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0470
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0870
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3861 r_free = 0.3861 target = 0.152752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.114556 restraints weight = 5838.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.59
r_work: 0.3270 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.3182

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= 0.119
  Angle     :  0.556   8.771   7949  Z= 0.292
  Chirality :  0.041   0.171    868
  Planarity :  0.004   0.088   1015
  Dihedral  :  4.693  22.848    768
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.69 %
    Favored  : 81.62 %
  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 aren not related in a simple way.
  whole:  0.31 (0.31), residues: 714
  helix:  1.49 (0.30), residues: 296
  sheet: -0.81 (0.84), residues: 40
  loop : -0.71 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   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   0.004   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5828)
  covalent geometry    : angle       0.54976 ( 7907)
  SS BOND              : bond        0.00164 (   21)
  SS BOND              : angle       1.26062 (   42)
  hydrogen bonds       : bond        0.03908 (  248)
  hydrogen bonds       : angle       4.84306 (  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
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7206 (t70) cc_final: 0.6474 (t70)
REVERT: A  610 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7008 (tpt90)
REVERT: B  363 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (ptp-170)
REVERT: B  489 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6917 (mp0)
REVERT: B  567 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7859 (mptm)
REVERT: B  620 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7844 (mp0)
REVERT: B  715 ARG cc_start: 0.7383 (tpt-90) cc_final: 0.7081 (tpm170)
REVERT: B  749 LEU cc_start: 0.8960 (mt) cc_final: 0.8715 (tp)
REVERT: B  770 TYR cc_start: 0.8384 (m-10) cc_final: 0.8116 (m-10)
  outliers start: 17
  outliers final: 11
  residues processed: 78
  average time/residue: 0.6934
  time to fit residues: 56.4297
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
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  369 ASP
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  419 SER
Chi-restraints excluded: chain B residue  489 GLU
Chi-restraints excluded: chain B residue  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3830 r_free = 0.3830 target = 0.150066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.111541 restraints weight = 5689.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.57
r_work: 0.3229 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5849  Z= 0.171
  Angle     :  0.617   8.780   7949  Z= 0.324
  Chirality :  0.043   0.174    868
  Planarity :  0.005   0.084   1015
  Dihedral  :  4.925  22.593    768
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.69 %
    Favored  : 81.62 %
  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 aren not related in a simple way.
  whole:  0.18 (0.30), residues: 714
  helix:  1.35 (0.30), residues: 295
  sheet: -1.25 (0.77), residues: 45
  loop : -0.70 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 610 
 TYR   0.012   0.002   TYR B 340 
 PHE   0.015   0.002   PHE B 668 
 TRP   0.010   0.002   TRP B 629 
 HIS   0.004   0.001   HIS B 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5828)
  covalent geometry    : angle       0.60989 ( 7907)
  SS BOND              : bond        0.00228 (   21)
  SS BOND              : angle       1.43174 (   42)
  hydrogen bonds       : bond        0.04629 (  248)
  hydrogen bonds       : angle       5.00810 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2999.04 seconds
wall clock time: 51 minutes 52.90 seconds (3112.90 seconds total)