Starting phenix.real_space_refine
on Tue Mar  3 13:49:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2026/7slp_25197.map"
  }
  resolution = 4.1
  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=   0.005
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      37      5.49       5
     S      15      5.16       5
     C    3151      2.51       5
     N     912      2.21       5
     O    1061      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  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: 5176
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1887
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 223}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 49
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2481
          Classifications: {'peptide': 321}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 10, 'TRANS': 310}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 69
    Chain: "R"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 782
          Classifications: {'RNA': 37}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 10, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 12, 'rna3p': 24}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.31, per 1000 atoms: 0.25
  Number of scatterers: 5176
  At special positions: 0
  Unit cell: (81.32, 78.11, 101.65, 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      15     16.00
     P      37     15.00
     O    1061      8.00
     N     912      7.00
     C    3151      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: 0.44
  Conformation dependent library (CDL) restraints added in 292.8 milliseconds
  

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1058

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 4 sheets defined
      49.8% alpha, 11.4% beta
      8 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.788A  pdb=" N   VAL A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 437 " --> pdb=" O   ARG A 433 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 432 through 437'
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 4.336A  pdb=" N   TRP A 441 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 465
    Processing helix  chain 'A' and resid 476 through 492
      removed outlier: 4.035A  pdb=" N   SER A 482 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR A 490 " --> pdb=" O   ASN A 486 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 532
      removed outlier: 3.614A  pdb=" N   THR A 528 " --> pdb=" O   PRO A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 569
    Processing helix  chain 'A' and resid 583 through 592
    Processing helix  chain 'A' and resid 593 through 606
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.872A  pdb=" N   TYR A 634 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 653
      removed outlier: 3.582A  pdb=" N   THR A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 46
    Processing helix  chain 'B' and resid 47 through 54
    Processing helix  chain 'B' and resid 55 through 63
    Processing helix  chain 'B' and resid 71 through 76
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 3.537A  pdb=" N   LYS B  82 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 94
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 176 through 186
      removed outlier: 3.502A  pdb=" N   GLU B 184 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 413
    Processing helix  chain 'B' and resid 467 through 479
      removed outlier: 3.967A  pdb=" N   ILE B 478 " --> pdb=" O   THR B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 508
    Processing helix  chain 'B' and resid 509 through 515
      removed outlier: 3.810A  pdb=" N   ILE B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 545
      removed outlier: 4.103A  pdb=" N   GLN B 530 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 571
    Processing sheet with id=AA1, first strand: chain 'A' and resid 554 through 557
      removed outlier: 6.611A  pdb=" N   MET A 470 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   VAL A 556 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLY A 472 " --> pdb=" O   VAL A 556 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU A 448 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   LEU A 581 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A 450 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ASP A 576 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   VAL A 614 " --> pdb=" O   ASP A 576 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL A 578 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   GLU A 616 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   CYS A 580 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 70
      removed outlier: 3.765A  pdb=" N   VAL B  69 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLU B 101 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 153 through 155
      removed outlier: 3.749A  pdb=" N   TYR B 153 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 485
      removed outlier: 6.360A  pdb=" N   ARG B 496 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL B 484 " --> pdb=" O   HIS B 494 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   HIS B 494 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)

    197 hydrogen bonds defined for protein.
    582 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1067
        1.33 -     1.45: 1463
        1.45 -     1.57: 2736
        1.57 -     1.70: 73
        1.70 -     1.82: 21
  Bond restraints: 5360
  Sorted by residual:
  bond pdb=" N   GLU A 574 "
       pdb=" CA  GLU A 574 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.00e-02 1.00e+04 9.22e+00
  bond pdb=" C2  SAH A 701 "
       pdb=" N3  SAH A 701 "
    ideal  model  delta    sigma   weight residual
    1.322  1.381 -0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" N   LYS A 625 "
       pdb=" CA  LYS A 625 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.29e-02 6.01e+03 8.37e+00
  bond pdb=" N   SER A 622 "
       pdb=" CA  SER A 622 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.89e+00
  bond pdb=" N   LYS B 112 "
       pdb=" CA  LYS B 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.23e+00
  ... (remaining 5355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 6922
        2.16 -     4.32: 427
        4.32 -     6.48: 62
        6.48 -     8.64: 16
        8.64 -    10.79: 9
  Bond angle restraints: 7436
  Sorted by residual:
  angle pdb=" N   LEU B 131 "
        pdb=" CA  LEU B 131 "
        pdb=" C   LEU B 131 "
      ideal   model   delta    sigma   weight residual
     110.91  120.44   -9.53 1.17e+00 7.31e-01 6.64e+01
  angle pdb=" C   PRO A 573 "
        pdb=" CA  PRO A 573 "
        pdb=" CB  PRO A 573 "
      ideal   model   delta    sigma   weight residual
     111.11  102.94    8.17 1.17e+00 7.31e-01 4.88e+01
  angle pdb=" C4'   G R 300 "
        pdb=" C3'   G R 300 "
        pdb=" O3'   G R 300 "
      ideal   model   delta    sigma   weight residual
     109.40  119.08   -9.68 1.50e+00 4.44e-01 4.16e+01
  angle pdb=" N   GLU B 480 "
        pdb=" CA  GLU B 480 "
        pdb=" C   GLU B 480 "
      ideal   model   delta    sigma   weight residual
     109.15  118.31   -9.16 1.44e+00 4.82e-01 4.05e+01
  angle pdb=" C   SER B 479 "
        pdb=" CA  SER B 479 "
        pdb=" CB  SER B 479 "
      ideal   model   delta    sigma   weight residual
     112.78  101.99   10.79 2.18e+00 2.10e-01 2.45e+01
  ... (remaining 7431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.54: 2895
       21.54 -    43.07: 262
       43.07 -    64.60: 88
       64.60 -    86.14: 24
       86.14 -   107.67: 7
  Dihedral angle restraints: 3276
    sinusoidal: 1641
      harmonic: 1635
  Sorted by residual:
  dihedral pdb=" CA  ASN A 426 "
           pdb=" C   ASN A 426 "
           pdb=" N   PRO A 427 "
           pdb=" CA  PRO A 427 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.43  -27.57     0      5.00e+00 4.00e-02 3.04e+01
  dihedral pdb=" CA  HIS A 682 "
           pdb=" C   HIS A 682 "
           pdb=" N   LYS A 683 "
           pdb=" CA  LYS A 683 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.21   23.79     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ARG B  55 "
           pdb=" C   ARG B  55 "
           pdb=" N   PHE B  56 "
           pdb=" CA  PHE B  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.35  -23.65     0      5.00e+00 4.00e-02 2.24e+01
  ... (remaining 3273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 733
       0.086 -    0.173: 115
       0.173 -    0.259: 16
       0.259 -    0.345: 1
       0.345 -    0.432: 2
  Chirality restraints: 867
  Sorted by residual:
  chirality pdb=" CB  VAL B  99 "
            pdb=" CA  VAL B  99 "
            pdb=" CG1 VAL B  99 "
            pdb=" CG2 VAL B  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.66e+00
  chirality pdb=" CA  PHE A 523 "
            pdb=" N   PHE A 523 "
            pdb=" C   PHE A 523 "
            pdb=" CB  PHE A 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  LEU B 131 "
            pdb=" N   LEU B 131 "
            pdb=" C   LEU B 131 "
            pdb=" CB  LEU B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 864 not shown)

  Planarity restraints: 807
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 643 "    0.043 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO A 644 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 644 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 644 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 539 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.04e+00
        pdb=" C   VAL A 539 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL A 539 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   PRO A 540 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 588 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.01e+00
        pdb=" C   HIS A 588 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   HIS A 588 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 589 "    0.014 2.00e-02 2.50e+03
  ... (remaining 804 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 814
        2.76 -     3.29: 4637
        3.29 -     3.83: 9027
        3.83 -     4.36: 9825
        4.36 -     4.90: 15905
  Nonbonded interactions: 40208
  Sorted by model distance:
  nonbonded pdb=" O2'   C R 320 "
            pdb=" OP1   C R 323 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O2'   U R 327 "
            pdb=" O2    U R 327 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   GLN B 470 "
            pdb=" OG1 THR B 474 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NH2 ARG B 552 "
            pdb=" N7    G R 303 "
     model   vdw
     2.303 3.200
  nonbonded pdb=" O   ARG A 425 "
            pdb=" OH  TYR A 490 "
     model   vdw
     2.306 3.040
  ... (remaining 40203 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 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:             0.520
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.300
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5588
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   0.100   5360  Z= 0.413
  Angle     :  1.220  10.794   7436  Z= 0.688
  Chirality :  0.067   0.432    867
  Planarity :  0.008   0.065    807
  Dihedral  : 19.399 107.672   2218
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  4.20 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.49 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -3.76 (0.27), residues: 548
  helix: -3.01 (0.21), residues: 266
  sheet:  0.07 (0.64), residues: 60
  loop : -2.38 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 484 
 TYR   0.029   0.005   TYR A 661 
 PHE   0.033   0.004   PHE A 442 
 TRP   0.018   0.003   TRP B 384 
 HIS   0.009   0.003   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00820 ( 5360)
  covalent geometry    : angle       1.21981 ( 7436)
  hydrogen bonds       : bond        0.18290 (  218)
  hydrogen bonds       : angle       7.77036 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  470 MET cc_start: 0.7272 (ttt) cc_final: 0.6917 (tmm)
REVERT: A  538 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7807 (mt0)
REVERT: A  557 THR cc_start: 0.6231 (t) cc_final: 0.5924 (t)
REVERT: A  582 SER cc_start: 0.6965 (m) cc_final: 0.6748 (t)
REVERT: A  607 LEU cc_start: 0.5854 (mt) cc_final: 0.5625 (mp)
REVERT: A  661 TYR cc_start: 0.6298 (p90) cc_final: 0.6024 (p90)
REVERT: B   50 ASN cc_start: 0.7391 (t0) cc_final: 0.7144 (t0)
REVERT: B  123 ASP cc_start: 0.8371 (t0) cc_final: 0.8168 (t0)
REVERT: B  159 TYR cc_start: 0.6892 (m-80) cc_final: 0.6436 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 158
  average time/residue: 0.0794
  time to fit residues: 15.8680
Evaluate side-chains
  89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:   30.0000
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 486 ASN
B  50 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.156564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.132984 restraints weight = 12318.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.135276 restraints weight = 8845.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.136801 restraints weight = 7053.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.137950 restraints weight = 5979.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.138686 restraints weight = 5321.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6186
moved from start:          0.4803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5360  Z= 0.162
  Angle     :  0.685   9.432   7436  Z= 0.349
  Chirality :  0.039   0.140    867
  Planarity :  0.007   0.081    807
  Dihedral  : 19.353 102.100   1201
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -1.58 (0.32), residues: 548
  helix: -0.81 (0.29), residues: 265
  sheet: -0.23 (0.70), residues: 50
  loop : -1.39 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 626 
 TYR   0.015   0.002   TYR A 650 
 PHE   0.017   0.003   PHE B  44 
 TRP   0.035   0.003   TRP A 586 
 HIS   0.008   0.002   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5360)
  covalent geometry    : angle       0.68484 ( 7436)
  hydrogen bonds       : bond        0.04632 (  218)
  hydrogen bonds       : angle       5.21971 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  449 ASP cc_start: 0.7054 (t0) cc_final: 0.6750 (t0)
REVERT: A  452 CYS cc_start: 0.7680 (p) cc_final: 0.6727 (p)
REVERT: A  582 SER cc_start: 0.7269 (m) cc_final: 0.6893 (t)
REVERT: A  608 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7208 (ptp-170)
REVERT: B   80 MET cc_start: 0.5455 (tpt) cc_final: 0.4666 (tpt)
REVERT: B  540 ARG cc_start: 0.5461 (ppt170) cc_final: 0.4923 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0875
  time to fit residues: 12.5392
Evaluate side-chains
  74 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.2980
   chunk 53 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B  50 ASN
B 408 GLN
B 530 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.154689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.129776 restraints weight = 11768.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.132343 restraints weight = 8092.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.134223 restraints weight = 6196.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.135474 restraints weight = 5111.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.135971 restraints weight = 4477.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.6767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5360  Z= 0.142
  Angle     :  0.651   8.737   7436  Z= 0.328
  Chirality :  0.038   0.142    867
  Planarity :  0.006   0.096    807
  Dihedral  : 19.049 100.929   1201
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.59 (0.34), residues: 548
  helix:  0.27 (0.31), residues: 262
  sheet:  0.02 (0.80), residues: 40
  loop : -1.14 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 626 
 TYR   0.016   0.002   TYR A 575 
 PHE   0.016   0.002   PHE A 523 
 TRP   0.031   0.002   TRP A 441 
 HIS   0.010   0.002   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5360)
  covalent geometry    : angle       0.65070 ( 7436)
  hydrogen bonds       : bond        0.04216 (  218)
  hydrogen bonds       : angle       4.84779 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 ASP cc_start: 0.7374 (t0) cc_final: 0.7012 (t0)
REVERT: A  582 SER cc_start: 0.7134 (m) cc_final: 0.6821 (t)
REVERT: A  608 ARG cc_start: 0.7559 (mtp85) cc_final: 0.6859 (ptp-170)
REVERT: B   80 MET cc_start: 0.5895 (tpt) cc_final: 0.5342 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0599
  time to fit residues: 8.3144
Evaluate side-chains
  75 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN
A 456 HIS
A 486 ASN
B 408 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.147708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121976 restraints weight = 12285.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.124388 restraints weight = 8545.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.126149 restraints weight = 6567.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127339 restraints weight = 5457.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.127974 restraints weight = 4794.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          1.0069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5360  Z= 0.222
  Angle     :  0.793  12.455   7436  Z= 0.397
  Chirality :  0.043   0.159    867
  Planarity :  0.007   0.095    807
  Dihedral  : 19.579  98.934   1201
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.19 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -1.01 (0.34), residues: 548
  helix: -0.02 (0.30), residues: 270
  sheet: -0.57 (0.65), residues: 56
  loop : -1.43 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  55 
 TYR   0.019   0.003   TYR A 604 
 PHE   0.018   0.003   PHE A 442 
 TRP   0.027   0.003   TRP B 519 
 HIS   0.012   0.003   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 5360)
  covalent geometry    : angle       0.79309 ( 7436)
  hydrogen bonds       : bond        0.05501 (  218)
  hydrogen bonds       : angle       5.66320 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: B  145 PHE cc_start: 0.7990 (m-10) cc_final: 0.7750 (m-10)
REVERT: B  383 GLU cc_start: 0.6748 (tt0) cc_final: 0.6502 (tt0)
REVERT: B  401 SER cc_start: 0.8658 (m) cc_final: 0.8402 (p)
REVERT: B  564 ILE cc_start: 0.9096 (tp) cc_final: 0.8884 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0557
  time to fit residues: 7.2885
Evaluate side-chains
  67 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0030
   chunk 56 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 481 HIS
A 489 HIS
** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN
B 517 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.151828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.125704 restraints weight = 12572.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.128243 restraints weight = 8764.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.130077 restraints weight = 6752.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.131219 restraints weight = 5616.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.132228 restraints weight = 4967.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          1.0619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5360  Z= 0.136
  Angle     :  0.601   8.488   7436  Z= 0.304
  Chirality :  0.039   0.126    867
  Planarity :  0.005   0.085    807
  Dihedral  : 18.901  95.252   1201
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  2.21 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.42 (0.35), residues: 548
  helix:  0.61 (0.32), residues: 271
  sheet: -0.86 (0.63), residues: 60
  loop : -1.16 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.018   0.002   TYR A 661 
 PHE   0.012   0.002   PHE B  44 
 TRP   0.038   0.002   TRP B 519 
 HIS   0.005   0.001   HIS A 606 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5360)
  covalent geometry    : angle       0.60089 ( 7436)
  hydrogen bonds       : bond        0.03999 (  218)
  hydrogen bonds       : angle       4.88777 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 ASP cc_start: 0.6824 (t70) cc_final: 0.6583 (t70)
REVERT: A  551 ASN cc_start: 0.8245 (p0) cc_final: 0.8013 (p0)
REVERT: B  540 ARG cc_start: 0.6798 (ppt170) cc_final: 0.6471 (ptm160)
REVERT: B  564 ILE cc_start: 0.9142 (tp) cc_final: 0.8860 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0680
  time to fit residues: 8.3179
Evaluate side-chains
  66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 481 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.151895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.126038 restraints weight = 12597.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.128618 restraints weight = 8692.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.130466 restraints weight = 6663.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.131839 restraints weight = 5480.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.132457 restraints weight = 4786.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          1.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5360  Z= 0.118
  Angle     :  0.587   8.395   7436  Z= 0.294
  Chirality :  0.038   0.132    867
  Planarity :  0.005   0.098    807
  Dihedral  : 18.661  94.533   1201
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.55 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.02 (0.36), residues: 548
  helix:  0.98 (0.32), residues: 270
  sheet: -0.05 (0.72), residues: 55
  loop : -1.21 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 484 
 TYR   0.012   0.001   TYR B 128 
 PHE   0.028   0.002   PHE A 600 
 TRP   0.017   0.002   TRP B 519 
 HIS   0.003   0.001   HIS A 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5360)
  covalent geometry    : angle       0.58656 ( 7436)
  hydrogen bonds       : bond        0.03636 (  218)
  hydrogen bonds       : angle       4.70125 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 ASP cc_start: 0.8051 (t0) cc_final: 0.7821 (t0)
REVERT: A  551 ASN cc_start: 0.8276 (p0) cc_final: 0.8034 (p0)
REVERT: A  593 ASP cc_start: 0.4376 (m-30) cc_final: 0.3119 (t70)
REVERT: B  540 ARG cc_start: 0.6970 (ppt170) cc_final: 0.6669 (ptm160)
REVERT: B  564 ILE cc_start: 0.9126 (tp) cc_final: 0.8835 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0570
  time to fit residues: 7.4643
Evaluate side-chains
  70 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 481 HIS
A 571 GLN
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 GLN
B 408 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.149157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123236 restraints weight = 12488.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.125546 restraints weight = 8936.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.127203 restraints weight = 7009.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.128372 restraints weight = 5880.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129260 restraints weight = 5197.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          1.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5360  Z= 0.146
  Angle     :  0.622   8.400   7436  Z= 0.309
  Chirality :  0.039   0.152    867
  Planarity :  0.006   0.103    807
  Dihedral  : 18.747  93.924   1201
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.99 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.07 (0.36), residues: 548
  helix:  0.88 (0.33), residues: 270
  sheet:  0.22 (0.79), residues: 48
  loop : -1.21 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  58 
 TYR   0.013   0.002   TYR B 532 
 PHE   0.017   0.002   PHE A 600 
 TRP   0.011   0.002   TRP A 586 
 HIS   0.003   0.001   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5360)
  covalent geometry    : angle       0.62212 ( 7436)
  hydrogen bonds       : bond        0.04048 (  218)
  hydrogen bonds       : angle       4.83154 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ASN cc_start: 0.8267 (p0) cc_final: 0.7996 (p0)
REVERT: A  593 ASP cc_start: 0.4879 (m-30) cc_final: 0.3730 (t70)
REVERT: B  390 GLU cc_start: 0.7985 (pp20) cc_final: 0.7567 (pp20)
REVERT: B  564 ILE cc_start: 0.9165 (tp) cc_final: 0.8843 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0569
  time to fit residues: 6.5849
Evaluate side-chains
  65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 481 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.148205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.121498 restraints weight = 12929.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.124041 restraints weight = 9025.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.125729 restraints weight = 6976.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.126734 restraints weight = 5850.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.127808 restraints weight = 5228.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          1.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5360  Z= 0.158
  Angle     :  0.633   7.236   7436  Z= 0.316
  Chirality :  0.039   0.131    867
  Planarity :  0.006   0.101    807
  Dihedral  : 18.799  95.259   1201
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.55 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.21 (0.36), residues: 548
  helix:  0.82 (0.32), residues: 270
  sheet: -0.12 (0.76), residues: 53
  loop : -1.30 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 598 
 TYR   0.012   0.002   TYR B 391 
 PHE   0.014   0.002   PHE B 185 
 TRP   0.012   0.002   TRP A 620 
 HIS   0.003   0.001   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 5360)
  covalent geometry    : angle       0.63274 ( 7436)
  hydrogen bonds       : bond        0.04078 (  218)
  hydrogen bonds       : angle       4.86972 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  551 ASN cc_start: 0.8295 (p0) cc_final: 0.8036 (p0)
REVERT: A  593 ASP cc_start: 0.4360 (m-30) cc_final: 0.3269 (t70)
REVERT: B  564 ILE cc_start: 0.9108 (tp) cc_final: 0.8802 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0574
  time to fit residues: 7.0169
Evaluate side-chains
  64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 HIS
A 486 ASN
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.147791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.123414 restraints weight = 12715.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.125353 restraints weight = 9491.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.126766 restraints weight = 7712.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.127771 restraints weight = 6639.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.128312 restraints weight = 5989.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          1.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5360  Z= 0.152
  Angle     :  0.623   7.574   7436  Z= 0.312
  Chirality :  0.039   0.137    867
  Planarity :  0.006   0.103    807
  Dihedral  : 18.891  95.089   1201
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.66 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.12 (0.36), residues: 548
  helix:  0.89 (0.32), residues: 269
  sheet:  0.07 (0.80), residues: 49
  loop : -1.26 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 484 
 TYR   0.012   0.002   TYR B 532 
 PHE   0.012   0.002   PHE B 185 
 TRP   0.014   0.002   TRP B 519 
 HIS   0.004   0.001   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5360)
  covalent geometry    : angle       0.62318 ( 7436)
  hydrogen bonds       : bond        0.04043 (  218)
  hydrogen bonds       : angle       4.86765 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  593 ASP cc_start: 0.4102 (m-30) cc_final: 0.3336 (t70)
REVERT: B   80 MET cc_start: 0.6803 (tpp) cc_final: 0.6345 (tpt)
REVERT: B  564 ILE cc_start: 0.9129 (tp) cc_final: 0.8813 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0525
  time to fit residues: 6.0479
Evaluate side-chains
  62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 481 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.149072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123408 restraints weight = 12927.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.125805 restraints weight = 9066.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127488 restraints weight = 7072.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.128605 restraints weight = 5950.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.129523 restraints weight = 5273.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          1.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5360  Z= 0.129
  Angle     :  0.599   7.857   7436  Z= 0.297
  Chirality :  0.038   0.129    867
  Planarity :  0.006   0.104    807
  Dihedral  : 18.777  94.836   1201
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.22 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.02 (0.37), residues: 548
  helix:  1.01 (0.33), residues: 270
  sheet:  0.16 (0.78), residues: 51
  loop : -1.22 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 540 
 TYR   0.012   0.001   TYR B 391 
 PHE   0.014   0.002   PHE A 658 
 TRP   0.011   0.002   TRP A 620 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5360)
  covalent geometry    : angle       0.59886 ( 7436)
  hydrogen bonds       : bond        0.03652 (  218)
  hydrogen bonds       : angle       4.69773 (  616)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  593 ASP cc_start: 0.4287 (m-30) cc_final: 0.3589 (t70)
REVERT: B   80 MET cc_start: 0.6889 (tpp) cc_final: 0.6551 (tpt)
REVERT: B  540 ARG cc_start: 0.6718 (tmt170) cc_final: 0.5854 (ptm-80)
REVERT: B  564 ILE cc_start: 0.9092 (tp) cc_final: 0.8779 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0572
  time to fit residues: 6.7491
Evaluate side-chains
  63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0170
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 HIS
B 408 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.152183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.127487 restraints weight = 13028.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129832 restraints weight = 9317.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.131532 restraints weight = 7320.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.132638 restraints weight = 6114.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133544 restraints weight = 5426.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          1.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5360  Z= 0.095
  Angle     :  0.552   7.638   7436  Z= 0.269
  Chirality :  0.037   0.124    867
  Planarity :  0.005   0.103    807
  Dihedral  : 18.380  94.068   1201
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.39 (0.37), residues: 548
  helix:  1.33 (0.33), residues: 270
  sheet:  0.36 (0.77), residues: 51
  loop : -1.07 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 478 
 TYR   0.013   0.001   TYR B 128 
 PHE   0.014   0.002   PHE B 185 
 TRP   0.010   0.002   TRP A 465 
 HIS   0.002   0.001   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 5360)
  covalent geometry    : angle       0.55191 ( 7436)
  hydrogen bonds       : bond        0.03140 (  218)
  hydrogen bonds       : angle       4.40124 (  616)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 963.71 seconds
wall clock time: 17 minutes 17.66 seconds (1037.66 seconds total)