Starting phenix.real_space_refine
on Tue Mar  3 15:36:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxi_32880/03_2026/7wxi_32880.map"
  }
  resolution = 4.2
  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=   0.004
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
     P       2      5.49       5
     S      30      5.16       5
     C    4064      2.51       5
     N    1174      2.21       5
     O    1252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6522
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3247
          Classifications: {'peptide': 430}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 414}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Classifications: {'peptide': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.61, per 1000 atoms: 0.25
  Number of scatterers: 6522
  At special positions: 0
  Unit cell: (98.58, 92.22, 62.54, 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)
     S      30     16.00
     P       2     15.00
     O    1252      8.00
     N    1174      7.00
     C    4064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.59
  Conformation dependent library (CDL) restraints added in 373.2 milliseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  RGP A 801 "
        pdb=" CB  RGP B 801 "
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 12 sheets defined
      50.1% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 364
      removed outlier: 4.096A  pdb=" N   ALA A 364 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 384
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 3.777A  pdb=" N   LYS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 412
    Processing helix  chain 'A' and resid 415 through 433
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 4.331A  pdb=" N   VAL A 513 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 534
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
      removed outlier: 3.772A  pdb=" N   ALA A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 613
    Processing helix  chain 'A' and resid 614 through 626
    Processing helix  chain 'A' and resid 633 through 640
    Processing helix  chain 'A' and resid 666 through 677
    Processing helix  chain 'A' and resid 689 through 700
      removed outlier: 3.626A  pdb=" N   ALA A 693 " --> pdb=" O   ASN A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 714
      removed outlier: 3.628A  pdb=" N   ALA A 714 " --> pdb=" O   SER A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 720
    Processing helix  chain 'A' and resid 739 through 744
    Processing helix  chain 'A' and resid 757 through 761
    Processing helix  chain 'B' and resid 348 through 364
      removed outlier: 4.096A  pdb=" N   ALA B 364 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 384
    Processing helix  chain 'B' and resid 384 through 401
      removed outlier: 3.777A  pdb=" N   LYS B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 412
    Processing helix  chain 'B' and resid 415 through 433
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 4.331A  pdb=" N   VAL B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 534
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 579 through 592
      removed outlier: 3.772A  pdb=" N   ALA B 583 " --> pdb=" O   ASP B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
    Processing helix  chain 'B' and resid 614 through 626
    Processing helix  chain 'B' and resid 633 through 640
    Processing helix  chain 'B' and resid 666 through 677
    Processing helix  chain 'B' and resid 689 through 700
      removed outlier: 3.626A  pdb=" N   ALA B 693 " --> pdb=" O   ASN B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 714
      removed outlier: 3.628A  pdb=" N   ALA B 714 " --> pdb=" O   SER B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 720
    Processing helix  chain 'B' and resid 739 through 744
    Processing helix  chain 'B' and resid 757 through 761
    Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751
      removed outlier: 4.420A  pdb=" N   GLU A 451 " --> pdb=" O   GLU A 751 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 771 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 457
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 490
      removed outlier: 6.555A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS A 490 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL A 464 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 607
      removed outlier: 5.647A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630
      removed outlier: 6.895A  pdb=" N   LYS A 629 " --> pdb=" O   CYS A 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728
    Processing sheet with id=AA7, first strand: chain 'B' and resid 750 through 751
      removed outlier: 4.420A  pdb=" N   GLU B 451 " --> pdb=" O   GLU B 751 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU B 771 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 457
    Processing sheet with id=AA9, first strand: chain 'B' and resid 487 through 490
      removed outlier: 6.555A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL B 464 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU B 463 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 605 through 607
      removed outlier: 5.647A  pdb=" N   ILE B 606 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 629 through 630
      removed outlier: 6.895A  pdb=" N   LYS B 629 " --> pdb=" O   CYS B 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 727 through 728

    300 hydrogen bonds defined for protein.
    822 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: 0.72 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1140
        1.31 -     1.43: 1536
        1.43 -     1.56: 3896
        1.56 -     1.68: 2
        1.68 -     1.81: 46
  Bond restraints: 6620
  Sorted by residual:
  bond pdb=" OE2 RGP A 801 "
       pdb=" PA  RGP A 801 "
    ideal  model  delta    sigma   weight residual
    1.798  1.646  0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" OE2 RGP B 801 "
       pdb=" PA  RGP B 801 "
    ideal  model  delta    sigma   weight residual
    1.798  1.646  0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" CD  RGP A 801 "
       pdb=" OE2 RGP A 801 "
    ideal  model  delta    sigma   weight residual
    1.302  1.395 -0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" CD  RGP B 801 "
       pdb=" OE2 RGP B 801 "
    ideal  model  delta    sigma   weight residual
    1.302  1.395 -0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" N   VAL A 455 "
       pdb=" CA  VAL A 455 "
    ideal  model  delta    sigma   weight residual
    1.459  1.437  0.022 1.25e-02 6.40e+03 3.13e+00
  ... (remaining 6615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8772
        2.32 -     4.64: 150
        4.64 -     6.95: 34
        6.95 -     9.27: 6
        9.27 -    11.59: 2
  Bond angle restraints: 8964
  Sorted by residual:
  angle pdb=" OE2 RGP B 801 "
        pdb=" PA  RGP B 801 "
        pdb=" OA3 RGP B 801 "
      ideal   model   delta    sigma   weight residual
      97.78  109.37  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" OE2 RGP A 801 "
        pdb=" PA  RGP A 801 "
        pdb=" OA3 RGP A 801 "
      ideal   model   delta    sigma   weight residual
      97.78  109.37  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" CG  RGP B 801 "
        pdb=" CD  RGP B 801 "
        pdb=" OE2 RGP B 801 "
      ideal   model   delta    sigma   weight residual
     112.09  119.96   -7.87 3.00e+00 1.11e-01 6.89e+00
  angle pdb=" CG  RGP A 801 "
        pdb=" CD  RGP A 801 "
        pdb=" OE2 RGP A 801 "
      ideal   model   delta    sigma   weight residual
     112.09  119.96   -7.87 3.00e+00 1.11e-01 6.89e+00
  angle pdb=" N   ARG A 544 "
        pdb=" CA  ARG A 544 "
        pdb=" C   ARG A 544 "
      ideal   model   delta    sigma   weight residual
     114.75  111.53    3.22 1.26e+00 6.30e-01 6.53e+00
  ... (remaining 8959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 3506
       16.01 -    32.02: 416
       32.02 -    48.02: 98
       48.02 -    64.03: 18
       64.03 -    80.04: 14
  Dihedral angle restraints: 4052
    sinusoidal: 1588
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  ILE A 732 "
           pdb=" C   ILE A 732 "
           pdb=" N   HIS A 733 "
           pdb=" CA  HIS A 733 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.31   21.69     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  ILE B 732 "
           pdb=" C   ILE B 732 "
           pdb=" N   HIS B 733 "
           pdb=" CA  HIS B 733 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.31   21.69     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  THR A 366 "
           pdb=" C   THR A 366 "
           pdb=" N   PRO A 367 "
           pdb=" CA  PRO A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.54  -21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 562
       0.030 -    0.059: 276
       0.059 -    0.089: 136
       0.089 -    0.118: 52
       0.118 -    0.148: 22
  Chirality restraints: 1048
  Sorted by residual:
  chirality pdb=" CA  ILE A 574 "
            pdb=" N   ILE A 574 "
            pdb=" C   ILE A 574 "
            pdb=" CB  ILE A 574 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  ILE B 574 "
            pdb=" N   ILE B 574 "
            pdb=" C   ILE B 574 "
            pdb=" CB  ILE B 574 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  VAL B 519 "
            pdb=" N   VAL B 519 "
            pdb=" C   VAL B 519 "
            pdb=" CB  VAL B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1045 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 643 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO B 644 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 644 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 644 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 643 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 644 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 644 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 644 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 664 "    0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO B 665 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 665 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 665 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 364
        2.70 -     3.25: 7708
        3.25 -     3.80: 10395
        3.80 -     4.35: 12380
        4.35 -     4.90: 20239
  Nonbonded interactions: 51086
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 429 "
            pdb=" OG  SER A 433 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   ILE B 429 "
            pdb=" OG  SER B 433 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   ALA A 509 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA B 509 "
            pdb=" OG1 THR B 512 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   CYS B 570 "
            pdb=" ND1 HIS B 571 "
     model   vdw
     2.224 3.120
  ... (remaining 51081 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             1.900
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.260
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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      :  0.008   0.152   6620  Z= 0.363
  Angle     :  0.875  11.589   8964  Z= 0.460
  Chirality :  0.046   0.148   1048
  Planarity :  0.005   0.043   1174
  Dihedral  : 15.473  80.038   2456
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 24.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.22 %
    Favored  : 81.78 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.88 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.77 (0.24), residues: 856
  helix: -2.25 (0.22), residues: 354
  sheet: -4.26 (0.37), residues: 112
  loop : -3.68 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 551 
 TYR   0.011   0.002   TYR A 654 
 PHE   0.009   0.002   PHE B 387 
 TRP   0.003   0.001   TRP B 748 
 HIS   0.007   0.002   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00762 ( 6620)
  covalent geometry    : angle       0.87497 ( 8964)
  hydrogen bonds       : bond        0.18356 (  300)
  hydrogen bonds       : angle       7.32348 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8727 (t80) cc_final: 0.8396 (t80)
REVERT: A  396 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (pp)
REVERT: A  487 LEU cc_start: 0.8871 (tp) cc_final: 0.8669 (tp)
REVERT: A  505 LEU cc_start: 0.7996 (mt) cc_final: 0.7767 (mt)
REVERT: A  534 MET cc_start: 0.8501 (tmm) cc_final: 0.7827 (tmm)
REVERT: A  577 ASP cc_start: 0.8501 (t70) cc_final: 0.8087 (t70)
REVERT: B  387 PHE cc_start: 0.8717 (t80) cc_final: 0.8386 (t80)
REVERT: B  505 LEU cc_start: 0.8076 (mt) cc_final: 0.7843 (mt)
REVERT: B  534 MET cc_start: 0.8501 (tmm) cc_final: 0.7813 (tmm)
REVERT: B  673 HIS cc_start: 0.8915 (t-90) cc_final: 0.8711 (t-170)
  outliers start: 4
  outliers final: 1
  residues processed: 135
  average time/residue: 0.0905
  time to fit residues: 15.7943
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 369 GLN
A 400 GLN
A 571 HIS
A 652 HIS
A 770 HIS
B 354 ASN
B 369 GLN
B 400 GLN
B 571 HIS
B 652 HIS
B 770 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.123350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.095109 restraints weight = 12025.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098452 restraints weight = 8061.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100809 restraints weight = 6080.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102569 restraints weight = 4994.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103712 restraints weight = 4318.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6620  Z= 0.190
  Angle     :  0.711   8.467   8964  Z= 0.373
  Chirality :  0.046   0.170   1048
  Planarity :  0.006   0.042   1174
  Dihedral  :  5.687  36.692    934
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.96 %
    Favored  : 92.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.27), residues: 856
  helix: -0.55 (0.25), residues: 372
  sheet: -3.72 (0.35), residues: 140
  loop : -3.07 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 525 
 TYR   0.009   0.002   TYR A 573 
 PHE   0.017   0.002   PHE A 760 
 TRP   0.008   0.002   TRP B 768 
 HIS   0.008   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6620)
  covalent geometry    : angle       0.71101 ( 8964)
  hydrogen bonds       : bond        0.04494 (  300)
  hydrogen bonds       : angle       5.13628 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8323 (t0)
REVERT: A  487 LEU cc_start: 0.8501 (tp) cc_final: 0.8299 (tp)
REVERT: A  505 LEU cc_start: 0.8144 (mt) cc_final: 0.7855 (mt)
REVERT: A  534 MET cc_start: 0.8440 (tmm) cc_final: 0.7919 (tmm)
REVERT: A  606 ILE cc_start: 0.8917 (mp) cc_final: 0.8646 (pt)
REVERT: A  662 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6822 (mm-30)
REVERT: A  724 GLU cc_start: 0.8614 (pp20) cc_final: 0.8297 (pt0)
REVERT: B  354 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8246 (t0)
REVERT: B  505 LEU cc_start: 0.8098 (mt) cc_final: 0.7842 (mt)
REVERT: B  534 MET cc_start: 0.8420 (tmm) cc_final: 0.7901 (tmm)
REVERT: B  724 GLU cc_start: 0.8601 (pp20) cc_final: 0.8265 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0656
  time to fit residues: 12.7622
Evaluate side-chains
  113 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 517 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.129548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.101598 restraints weight = 11448.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105027 restraints weight = 7576.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.107446 restraints weight = 5675.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109126 restraints weight = 4629.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110519 restraints weight = 3998.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6620  Z= 0.139
  Angle     :  0.650   8.747   8964  Z= 0.333
  Chirality :  0.043   0.161   1048
  Planarity :  0.005   0.039   1174
  Dihedral  :  5.302  36.036    934
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.28), residues: 856
  helix:  0.18 (0.26), residues: 372
  sheet: -3.08 (0.37), residues: 142
  loop : -2.66 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 525 
 TYR   0.007   0.001   TYR B 573 
 PHE   0.014   0.001   PHE A 616 
 TRP   0.006   0.001   TRP B 768 
 HIS   0.005   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6620)
  covalent geometry    : angle       0.64987 ( 8964)
  hydrogen bonds       : bond        0.03858 (  300)
  hydrogen bonds       : angle       4.70350 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  505 LEU cc_start: 0.7907 (mt) cc_final: 0.7364 (mp)
REVERT: A  558 LEU cc_start: 0.6742 (tp) cc_final: 0.5968 (tp)
REVERT: B  505 LEU cc_start: 0.7967 (mt) cc_final: 0.7533 (mp)
REVERT: B  662 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6887 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0667
  time to fit residues: 14.0608
Evaluate side-chains
  112 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0980
   chunk 83 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 475 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.132054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101947 restraints weight = 11515.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.105753 restraints weight = 7193.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108569 restraints weight = 5234.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110589 restraints weight = 4180.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111916 restraints weight = 3548.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6620  Z= 0.135
  Angle     :  0.692  10.927   8964  Z= 0.342
  Chirality :  0.045   0.369   1048
  Planarity :  0.005   0.038   1174
  Dihedral  :  5.119  35.550    934
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.28), residues: 856
  helix:  0.49 (0.26), residues: 376
  sheet: -2.76 (0.37), residues: 142
  loop : -2.46 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 585 
 TYR   0.009   0.001   TYR A 654 
 PHE   0.013   0.002   PHE A 760 
 TRP   0.005   0.001   TRP A 768 
 HIS   0.004   0.001   HIS B 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6620)
  covalent geometry    : angle       0.69178 ( 8964)
  hydrogen bonds       : bond        0.03561 (  300)
  hydrogen bonds       : angle       4.46238 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  505 LEU cc_start: 0.7871 (mt) cc_final: 0.7373 (mp)
REVERT: B  505 LEU cc_start: 0.7837 (mt) cc_final: 0.7429 (mp)
REVERT: B  526 GLU cc_start: 0.7431 (mp0) cc_final: 0.6929 (mp0)
REVERT: B  601 MET cc_start: 0.8402 (tmm) cc_final: 0.7584 (tmm)
REVERT: B  662 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6869 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0616
  time to fit residues: 14.0437
Evaluate side-chains
  122 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 71 optimal weight:    0.0570
   overall best weight:    0.4506

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 475 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102234 restraints weight = 11976.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106211 restraints weight = 7503.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109137 restraints weight = 5434.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111217 restraints weight = 4318.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.112804 restraints weight = 3656.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6620  Z= 0.129
  Angle     :  0.695   9.853   8964  Z= 0.341
  Chirality :  0.045   0.187   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  5.017  35.176    934
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.28), residues: 856
  helix:  0.55 (0.27), residues: 378
  sheet: -2.65 (0.36), residues: 142
  loop : -2.32 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 525 
 TYR   0.008   0.001   TYR A 654 
 PHE   0.021   0.002   PHE B 616 
 TRP   0.009   0.001   TRP B 748 
 HIS   0.006   0.001   HIS B 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6620)
  covalent geometry    : angle       0.69477 ( 8964)
  hydrogen bonds       : bond        0.03415 (  300)
  hydrogen bonds       : angle       4.37719 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 CYS cc_start: 0.8234 (m) cc_final: 0.8032 (m)
REVERT: A  695 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: B  353 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8620 (mm-30)
REVERT: B  505 LEU cc_start: 0.7834 (mt) cc_final: 0.7414 (mp)
REVERT: B  601 MET cc_start: 0.8626 (tmm) cc_final: 0.8219 (tmm)
REVERT: B  622 MET cc_start: 0.8572 (tmm) cc_final: 0.8138 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0525
  time to fit residues: 11.9904
Evaluate side-chains
  115 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 475 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.131786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.101370 restraints weight = 12007.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.105264 restraints weight = 7657.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.108120 restraints weight = 5609.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110206 restraints weight = 4481.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111582 restraints weight = 3792.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6620  Z= 0.135
  Angle     :  0.677   9.697   8964  Z= 0.336
  Chirality :  0.044   0.173   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  4.955  34.763    934
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.28), residues: 856
  helix:  0.71 (0.26), residues: 378
  sheet: -2.41 (0.36), residues: 142
  loop : -2.29 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 625 
 TYR   0.008   0.001   TYR A 654 
 PHE   0.010   0.001   PHE A 696 
 TRP   0.011   0.002   TRP A 748 
 HIS   0.006   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6620)
  covalent geometry    : angle       0.67721 ( 8964)
  hydrogen bonds       : bond        0.03354 (  300)
  hydrogen bonds       : angle       4.38722 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  503 MET cc_start: 0.7691 (tpt) cc_final: 0.6883 (tmm)
REVERT: A  570 CYS cc_start: 0.8231 (m) cc_final: 0.8005 (m)
REVERT: A  695 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8663 (tm-30)
REVERT: B  353 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8646 (mm-30)
REVERT: B  505 LEU cc_start: 0.7806 (mt) cc_final: 0.7231 (mp)
REVERT: B  601 MET cc_start: 0.8576 (tmm) cc_final: 0.8141 (tmm)
REVERT: B  662 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7208 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0527
  time to fit residues: 11.4277
Evaluate side-chains
  115 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 475 GLN
A 565 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.131885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101698 restraints weight = 11860.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.105583 restraints weight = 7574.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108357 restraints weight = 5539.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.110449 restraints weight = 4443.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.111602 restraints weight = 3772.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6620  Z= 0.133
  Angle     :  0.681   8.736   8964  Z= 0.335
  Chirality :  0.044   0.166   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  4.902  34.383    934
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.29), residues: 856
  helix:  0.86 (0.26), residues: 378
  sheet: -2.19 (0.38), residues: 142
  loop : -2.20 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 625 
 TYR   0.008   0.001   TYR A 573 
 PHE   0.026   0.002   PHE B 616 
 TRP   0.007   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6620)
  covalent geometry    : angle       0.68071 ( 8964)
  hydrogen bonds       : bond        0.03252 (  300)
  hydrogen bonds       : angle       4.33229 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 PHE cc_start: 0.8537 (t80) cc_final: 0.8307 (t80)
REVERT: B  353 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8651 (mm-30)
REVERT: B  601 MET cc_start: 0.8541 (tmm) cc_final: 0.8097 (tmm)
REVERT: B  662 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7223 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0537
  time to fit residues: 12.2784
Evaluate side-chains
  117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 85 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0670
   chunk 81 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 392 ASN
** B 565 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.134274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104177 restraints weight = 11939.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108178 restraints weight = 7652.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111129 restraints weight = 5577.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113195 restraints weight = 4455.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114760 restraints weight = 3787.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6620  Z= 0.120
  Angle     :  0.677   9.646   8964  Z= 0.332
  Chirality :  0.044   0.176   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  4.787  34.386    934
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.29), residues: 856
  helix:  0.83 (0.26), residues: 378
  sheet: -2.05 (0.39), residues: 142
  loop : -2.05 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 635 
 TYR   0.006   0.001   TYR B 654 
 PHE   0.019   0.001   PHE A 616 
 TRP   0.005   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6620)
  covalent geometry    : angle       0.67656 ( 8964)
  hydrogen bonds       : bond        0.03153 (  300)
  hydrogen bonds       : angle       4.20381 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  353 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8568 (mm-30)
REVERT: B  428 GLN cc_start: 0.8788 (mp10) cc_final: 0.8553 (mp10)
REVERT: B  601 MET cc_start: 0.8496 (tmm) cc_final: 0.8078 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0526
  time to fit residues: 11.5489
Evaluate side-chains
  119 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 41 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 565 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.133699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103222 restraints weight = 11836.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107201 restraints weight = 7481.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110101 restraints weight = 5436.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112153 restraints weight = 4330.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113712 restraints weight = 3672.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6620  Z= 0.139
  Angle     :  0.688   9.285   8964  Z= 0.343
  Chirality :  0.044   0.172   1048
  Planarity :  0.004   0.040   1174
  Dihedral  :  4.793  34.121    934
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.29), residues: 856
  helix:  0.93 (0.26), residues: 378
  sheet: -2.11 (0.38), residues: 150
  loop : -2.00 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 635 
 TYR   0.009   0.001   TYR B 573 
 PHE   0.028   0.002   PHE B 616 
 TRP   0.006   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6620)
  covalent geometry    : angle       0.68754 ( 8964)
  hydrogen bonds       : bond        0.03128 (  300)
  hydrogen bonds       : angle       4.15259 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  570 CYS cc_start: 0.8144 (m) cc_final: 0.7931 (m)
REVERT: B  601 MET cc_start: 0.8488 (tmm) cc_final: 0.8048 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0581
  time to fit residues: 12.1573
Evaluate side-chains
  113 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.103176 restraints weight = 11581.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.107069 restraints weight = 7387.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.109954 restraints weight = 5399.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112045 restraints weight = 4306.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113551 restraints weight = 3639.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6620  Z= 0.146
  Angle     :  0.707   8.901   8964  Z= 0.352
  Chirality :  0.045   0.172   1048
  Planarity :  0.005   0.036   1174
  Dihedral  :  4.831  34.033    934
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.29), residues: 856
  helix:  0.86 (0.26), residues: 378
  sheet: -2.28 (0.39), residues: 140
  loop : -1.98 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 635 
 TYR   0.008   0.001   TYR A 654 
 PHE   0.024   0.001   PHE A 616 
 TRP   0.010   0.002   TRP B 768 
 HIS   0.004   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6620)
  covalent geometry    : angle       0.70742 ( 8964)
  hydrogen bonds       : bond        0.03159 (  300)
  hydrogen bonds       : angle       4.33271 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  624 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8986 (mttt)
REVERT: A  664 VAL cc_start: 0.8263 (t) cc_final: 0.7689 (t)
REVERT: B  353 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8389 (mm-30)
REVERT: B  537 HIS cc_start: 0.7516 (m90) cc_final: 0.7049 (m170)
REVERT: B  570 CYS cc_start: 0.8157 (m) cc_final: 0.7940 (m)
REVERT: B  601 MET cc_start: 0.8480 (tmm) cc_final: 0.8019 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0512
  time to fit residues: 10.9159
Evaluate side-chains
  114 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 60 optimal weight:    0.4980
   chunk 40 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0050
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104904 restraints weight = 11737.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108802 restraints weight = 7542.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.111557 restraints weight = 5519.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113729 restraints weight = 4433.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115130 restraints weight = 3754.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6620  Z= 0.127
  Angle     :  0.691   9.045   8964  Z= 0.345
  Chirality :  0.045   0.169   1048
  Planarity :  0.004   0.036   1174
  Dihedral  :  4.795  34.057    934
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.29), residues: 856
  helix:  0.74 (0.27), residues: 378
  sheet: -2.20 (0.37), residues: 166
  loop : -2.00 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 625 
 TYR   0.007   0.001   TYR A 654 
 PHE   0.024   0.001   PHE B 616 
 TRP   0.013   0.002   TRP B 768 
 HIS   0.004   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6620)
  covalent geometry    : angle       0.69098 ( 8964)
  hydrogen bonds       : bond        0.03215 (  300)
  hydrogen bonds       : angle       4.27713 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1057.27 seconds
wall clock time: 19 minutes 2.17 seconds (1142.17 seconds total)