Starting phenix.real_space_refine
on Thu Jun  5 08:13:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8snn_40630/06_2025/8snn_40630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8snn_40630/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8snn_40630/06_2025/8snn_40630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8snn_40630/06_2025/8snn_40630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8snn_40630/06_2025/8snn_40630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8snn_40630/06_2025/8snn_40630.cif"
  }
  resolution = 2.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.054
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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5685
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1745
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3939
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.91, per 1000 atoms: 1.57
  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: 2.86
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 0.64
  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: 2.97

  Time building geometry restraints manager: 3.34 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:             90.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     29.100
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:15.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  135.400
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (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
 TRP   0.012   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 556 
 PHE   0.012   0.001   PHE B 668 
 TYR   0.006   0.001   TYR B 820 
 ARG   0.004   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15671 (  248)
  hydrogen bonds       : angle       6.90586 (  711)
  SS BOND              : bond        0.00189 (   21)
  SS BOND              : angle       1.03518 (   42)
  covalent geometry    : bond        0.00337 ( 5828)
  covalent geometry    : angle       0.64137 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.638 
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: 1.1909
  time to fit residues: 160.4518
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  : 0.694 
-------------------------------------------------------------------------------
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 59 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 ASN
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 ASN
B 635 HIS
B 648 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.150143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111355 restraints weight = 5700.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.57
r_work: 0.3227 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   5849  Z= 0.225
  Angle     :  0.685   7.811   7949  Z= 0.360
  Chirality :  0.047   0.210    868
  Planarity :  0.005   0.044   1015
  Dihedral  :  5.461  57.118    770
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.51 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 714
  helix:  1.15 (0.30), residues: 285
  sheet: -0.91 (0.87), residues: 36
  loop : -0.62 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 710 
 HIS   0.006   0.001   HIS B 595 
 PHE   0.016   0.002   PHE B 783 
 TYR   0.018   0.002   TYR B 340 
 ARG   0.008   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05533 (  248)
  hydrogen bonds       : angle       5.50486 (  711)
  SS BOND              : bond        0.00412 (   21)
  SS BOND              : angle       1.54563 (   42)
  covalent geometry    : bond        0.00516 ( 5828)
  covalent geometry    : angle       0.67742 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A  523 LYS cc_start: 0.7794 (tptm) cc_final: 0.7055 (pmtt)
REVERT: A  616 ASP cc_start: 0.6635 (t0) cc_final: 0.6409 (t0)
REVERT: A  643 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8458 (mtpp)
REVERT: A  672 ILE cc_start: 0.9090 (mt) cc_final: 0.8836 (tp)
REVERT: A  697 LYS cc_start: 0.7546 (tttt) cc_final: 0.6528 (mptm)
REVERT: B  354 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7174 (mtm110)
REVERT: B  567 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7974 (mptm)
REVERT: B  749 LEU cc_start: 0.8979 (mt) cc_final: 0.8715 (tp)
REVERT: B  770 TYR cc_start: 0.8443 (m-10) cc_final: 0.8172 (m-80)
  outliers start: 16
  outliers final: 6
  residues processed: 88
  average time/residue: 1.4242
  time to fit residues: 130.7598
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ASP
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 68 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 3 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0010
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 621 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 722 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.152722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.113928 restraints weight = 5786.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.59
r_work: 0.3266 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2572

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= 0.139
  Angle     :  0.596  10.388   7949  Z= 0.313
  Chirality :  0.042   0.234    868
  Planarity :  0.004   0.047   1015
  Dihedral  :  5.243  53.338    770
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.30), residues: 714
  helix:  1.28 (0.30), residues: 293
  sheet: -0.90 (0.91), residues: 36
  loop : -0.73 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 556 
 PHE   0.015   0.001   PHE B 668 
 TYR   0.012   0.001   TYR B 340 
 ARG   0.010   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  248)
  hydrogen bonds       : angle       5.15969 (  711)
  SS BOND              : bond        0.00217 (   21)
  SS BOND              : angle       1.84698 (   42)
  covalent geometry    : bond        0.00313 ( 5828)
  covalent geometry    : angle       0.58268 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8634 (p) cc_final: 0.8226 (m)
REVERT: A  595 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6650 (pm20)
REVERT: A  616 ASP cc_start: 0.6527 (t0) cc_final: 0.6308 (t0)
REVERT: A  672 ILE cc_start: 0.9046 (mt) cc_final: 0.8817 (tp)
REVERT: B  354 ARG cc_start: 0.7551 (mtp180) cc_final: 0.7122 (mtm110)
REVERT: B  414 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7481 (mttp)
REVERT: B  567 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7894 (mptm)
REVERT: B  749 LEU cc_start: 0.8956 (mt) cc_final: 0.8700 (tp)
REVERT: B  770 TYR cc_start: 0.8436 (m-10) cc_final: 0.8182 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 78
  average time/residue: 1.3743
  time to fit residues: 111.9012
Evaluate side-chains
  72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  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  762 ILE
Chi-restraints excluded: chain B residue  769 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0980
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 20 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:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 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 = 0.3855 r_free = 0.3855 target = 0.152207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113449 restraints weight = 5816.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.59
r_work: 0.3258 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.2752

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= 0.138
  Angle     :  0.571   9.914   7949  Z= 0.300
  Chirality :  0.042   0.231    868
  Planarity :  0.004   0.052   1015
  Dihedral  :  4.842  24.382    768
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.00 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 714
  helix:  1.36 (0.30), residues: 295
  sheet: -0.89 (0.85), residues: 40
  loop : -0.67 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 429 
 HIS   0.005   0.001   HIS B 556 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.012   0.001   TYR B 340 
 ARG   0.014   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  248)
  hydrogen bonds       : angle       5.02432 (  711)
  SS BOND              : bond        0.00217 (   21)
  SS BOND              : angle       1.28787 (   42)
  covalent geometry    : bond        0.00310 ( 5828)
  covalent geometry    : angle       0.56526 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8670 (p) cc_final: 0.8317 (m)
REVERT: A  505 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6931 (p0)
REVERT: A  595 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6733 (pm20)
REVERT: A  672 ILE cc_start: 0.9044 (mt) cc_final: 0.8825 (tp)
REVERT: B  354 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7136 (mtm110)
REVERT: B  414 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7510 (mttp)
REVERT: B  489 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6844 (mp0)
REVERT: B  567 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7895 (mptm)
REVERT: B  749 LEU cc_start: 0.8966 (mt) cc_final: 0.8708 (tp)
REVERT: B  770 TYR cc_start: 0.8412 (m-10) cc_final: 0.8151 (m-10)
  outliers start: 21
  outliers final: 11
  residues processed: 80
  average time/residue: 1.2197
  time to fit residues: 102.1423
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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 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  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  567 LYS
Chi-restraints excluded: chain B residue  689 VAL
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 39 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 605 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.150749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.112006 restraints weight = 5767.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.58
r_work: 0.3233 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2950

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= 0.159
  Angle     :  0.595   9.152   7949  Z= 0.313
  Chirality :  0.043   0.193    868
  Planarity :  0.004   0.055   1015
  Dihedral  :  4.936  22.779    768
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.30), residues: 714
  helix:  1.29 (0.30), residues: 295
  sheet: -1.37 (0.84), residues: 41
  loop : -0.66 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 429 
 HIS   0.004   0.001   HIS B 556 
 PHE   0.014   0.002   PHE B 668 
 TYR   0.010   0.001   TYR B 593 
 ARG   0.014   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  248)
  hydrogen bonds       : angle       5.07322 (  711)
  SS BOND              : bond        0.00208 (   21)
  SS BOND              : angle       1.34381 (   42)
  covalent geometry    : bond        0.00361 ( 5828)
  covalent geometry    : angle       0.58856 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  504 SER cc_start: 0.8718 (p) cc_final: 0.8492 (m)
REVERT: A  505 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7213 (p0)
REVERT: A  595 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6750 (pm20)
REVERT: A  643 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8443 (mtpp)
REVERT: A  647 ASP cc_start: 0.6833 (t0) cc_final: 0.6549 (t0)
REVERT: A  672 ILE cc_start: 0.9015 (mt) cc_final: 0.8806 (tp)
REVERT: B  354 ARG cc_start: 0.7596 (mtp180) cc_final: 0.7195 (mtm110)
REVERT: B  414 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7530 (mttp)
REVERT: B  567 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8006 (mptm)
REVERT: B  770 TYR cc_start: 0.8429 (m-10) cc_final: 0.8173 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 82
  average time/residue: 1.3630
  time to fit residues: 117.0769
Evaluate side-chains
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  643 LYS
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 49 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.151798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.113565 restraints weight = 5710.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.56
r_work: 0.3261 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.3049

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= 0.132
  Angle     :  0.566   8.762   7949  Z= 0.297
  Chirality :  0.042   0.183    868
  Planarity :  0.004   0.067   1015
  Dihedral  :  4.791  22.705    768
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 714
  helix:  1.41 (0.30), residues: 295
  sheet: -1.35 (0.79), residues: 45
  loop : -0.64 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 556 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.017   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  248)
  hydrogen bonds       : angle       4.94543 (  711)
  SS BOND              : bond        0.00183 (   21)
  SS BOND              : angle       1.26696 (   42)
  covalent geometry    : bond        0.00297 ( 5828)
  covalent geometry    : angle       0.56034 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7244 (p0)
REVERT: A  595 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6746 (pm20)
REVERT: A  647 ASP cc_start: 0.6803 (t0) cc_final: 0.6537 (t0)
REVERT: A  672 ILE cc_start: 0.9018 (mt) cc_final: 0.8816 (tp)
REVERT: B  354 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7168 (mtm110)
REVERT: B  363 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7356 (ptp-170)
REVERT: B  414 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7486 (mttp)
REVERT: B  489 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6886 (mp0)
REVERT: B  567 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7896 (mptm)
REVERT: B  749 LEU cc_start: 0.8945 (mt) cc_final: 0.8697 (tp)
REVERT: B  770 TYR cc_start: 0.8432 (m-10) cc_final: 0.8164 (m-10)
  outliers start: 21
  outliers final: 11
  residues processed: 79
  average time/residue: 2.1401
  time to fit residues: 177.4744
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 2.542 
-------------------------------------------------------------------------------
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  369 ASP
Chi-restraints excluded: chain B residue  370 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0570
   chunk 15 optimal weight:    0.0770
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   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 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.153162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.114915 restraints weight = 5768.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.58
r_work: 0.3276 rms_B_bonded: 2.06 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: 0.8679
moved from start:          0.3097

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= 0.117
  Angle     :  0.539   8.662   7949  Z= 0.282
  Chirality :  0.041   0.175    868
  Planarity :  0.004   0.072   1015
  Dihedral  :  4.626  22.608    768
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.74 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.31), residues: 714
  helix:  1.52 (0.30), residues: 295
  sheet: -0.87 (0.84), residues: 40
  loop : -0.63 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 556 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.010   0.001   TYR B 340 
 ARG   0.016   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  248)
  hydrogen bonds       : angle       4.82739 (  711)
  SS BOND              : bond        0.00153 (   21)
  SS BOND              : angle       1.18799 (   42)
  covalent geometry    : bond        0.00259 ( 5828)
  covalent geometry    : angle       0.53320 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  505 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7387 (p0)
REVERT: A  595 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6838 (pm20)
REVERT: A  610 ARG cc_start: 0.7912 (ttm110) cc_final: 0.6924 (tpt90)
REVERT: B  354 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7163 (mtm110)
REVERT: B  363 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7431 (ptp-170)
REVERT: B  567 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7869 (mptm)
REVERT: B  749 LEU cc_start: 0.8945 (mt) cc_final: 0.8705 (tp)
REVERT: B  770 TYR cc_start: 0.8442 (m-10) cc_final: 0.8169 (m-10)
  outliers start: 19
  outliers final: 10
  residues processed: 79
  average time/residue: 1.6877
  time to fit residues: 139.6631
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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  493 THR
Chi-restraints excluded: chain B residue  567 LYS
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 13 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 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 = 0.151334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.113230 restraints weight = 5647.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.55
r_work: 0.3252 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5849  Z= 0.143
  Angle     :  0.571   8.717   7949  Z= 0.300
  Chirality :  0.042   0.176    868
  Planarity :  0.004   0.062   1015
  Dihedral  :  4.743  22.465    768
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.31), residues: 714
  helix:  1.42 (0.30), residues: 295
  sheet: -1.33 (0.77), residues: 45
  loop : -0.61 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 556 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.014   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  248)
  hydrogen bonds       : angle       4.92192 (  711)
  SS BOND              : bond        0.00177 (   21)
  SS BOND              : angle       1.28299 (   42)
  covalent geometry    : bond        0.00321 ( 5828)
  covalent geometry    : angle       0.56498 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7084 (t70) cc_final: 0.6527 (t70)
REVERT: A  505 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7397 (p0)
REVERT: B  354 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7175 (mtm110)
REVERT: B  363 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7425 (ptp-170)
REVERT: B  567 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7891 (mptm)
REVERT: B  770 TYR cc_start: 0.8412 (m-10) cc_final: 0.8148 (m-10)
  outliers start: 17
  outliers final: 12
  residues processed: 75
  average time/residue: 1.4765
  time to fit residues: 115.6235
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
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  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  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 8 optimal weight:    0.0570
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 ASN ** 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 = 0.3837 r_free = 0.3837 target = 0.150645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112300 restraints weight = 5748.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.57
r_work: 0.3241 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3224

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= 0.149
  Angle     :  0.588   8.755   7949  Z= 0.309
  Chirality :  0.042   0.174    868
  Planarity :  0.004   0.081   1015
  Dihedral  :  4.834  22.591    768
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.69 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.30), residues: 714
  helix:  1.34 (0.30), residues: 296
  sheet: -1.30 (0.78), residues: 45
  loop : -0.65 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 
 PHE   0.015   0.001   PHE B 668 
 TYR   0.012   0.001   TYR B 340 
 ARG   0.019   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  248)
  hydrogen bonds       : angle       4.96803 (  711)
  SS BOND              : bond        0.00185 (   21)
  SS BOND              : angle       1.33844 (   42)
  covalent geometry    : bond        0.00338 ( 5828)
  covalent geometry    : angle       0.58144 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7221 (t70) cc_final: 0.6547 (t70)
REVERT: A  610 ARG cc_start: 0.7914 (ttm110) cc_final: 0.6975 (tpt90)
REVERT: B  363 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7466 (ptp-170)
REVERT: B  567 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7937 (mptm)
REVERT: B  770 TYR cc_start: 0.8432 (m-10) cc_final: 0.8171 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 77
  average time/residue: 1.3986
  time to fit residues: 112.4008
Evaluate side-chains
  75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   chunk 68 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.151544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113616 restraints weight = 5770.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.56
r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3223

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= 0.129
  Angle     :  0.566   8.869   7949  Z= 0.297
  Chirality :  0.042   0.170    868
  Planarity :  0.004   0.082   1015
  Dihedral  :  4.747  22.659    768
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.01 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.30), residues: 714
  helix:  1.40 (0.30), residues: 295
  sheet: -0.81 (0.85), residues: 40
  loop : -0.70 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.019   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  248)
  hydrogen bonds       : angle       4.88124 (  711)
  SS BOND              : bond        0.00174 (   21)
  SS BOND              : angle       1.28112 (   42)
  covalent geometry    : bond        0.00288 ( 5828)
  covalent geometry    : angle       0.55943 ( 7907)

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

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.7158 (t70) cc_final: 0.6469 (t70)
REVERT: A  610 ARG cc_start: 0.7904 (ttm110) cc_final: 0.6960 (tpt90)
REVERT: B  363 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7441 (ptp-170)
REVERT: B  567 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7887 (mptm)
REVERT: B  749 LEU cc_start: 0.8972 (mt) cc_final: 0.8721 (tp)
REVERT: B  770 TYR cc_start: 0.8424 (m-10) cc_final: 0.8164 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 75
  average time/residue: 1.2561
  time to fit residues: 98.6785
Evaluate side-chains
  75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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  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  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 20 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 70 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.151678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113497 restraints weight = 5763.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.58
r_work: 0.3257 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
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      :  0.003   0.040   5849  Z= 0.128
  Angle     :  0.564   8.794   7949  Z= 0.296
  Chirality :  0.042   0.173    868
  Planarity :  0.004   0.078   1015
  Dihedral  :  4.725  22.595    768
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.48 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.30), residues: 714
  helix:  1.42 (0.30), residues: 295
  sheet: -1.28 (0.78), residues: 45
  loop : -0.66 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 429 
 HIS   0.003   0.001   HIS B 635 
 PHE   0.014   0.001   PHE B 668 
 TYR   0.010   0.001   TYR B 340 
 ARG   0.018   0.001   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  248)
  hydrogen bonds       : angle       4.87619 (  711)
  SS BOND              : bond        0.00162 (   21)
  SS BOND              : angle       1.29090 (   42)
  covalent geometry    : bond        0.00286 ( 5828)
  covalent geometry    : angle       0.55791 ( 7907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6969.50 seconds
wall clock time: 122 minutes 47.28 seconds (7367.28 seconds total)