Starting phenix.real_space_refine
on Tue Feb  3 15:33:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9opx_70729/02_2026/9opx_70729.cif"
  }
  resolution = 3.63
  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=   0.005 sd=   0.080
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: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    2888      2.51       5
     N     682      2.21       5
     O     719      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4327
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2182
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 17, 'TRANS': 260}
    Chain: "B"
      Number of atoms: 2145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2145
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 16, 'TRANS': 258}
  Time building chain proxies: 0.99, per 1000 atoms: 0.23
  Number of scatterers: 4327
  At special positions: 0
  Unit cell: (76.582, 85.668, 90.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O     719      8.00
     N     682      7.00
     C    2888      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: 0.38
  Conformation dependent library (CDL) restraints added in 170.6 milliseconds
  

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1050

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      81.9% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 563 through 590
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 601 through 616
      removed outlier: 3.574A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   MET A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 622
    Processing helix  chain 'A' and resid 626 through 635
    Processing helix  chain 'A' and resid 635 through 665
      removed outlier: 3.509A  pdb=" N   CYS A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS A 644 " --> pdb=" O   CYS A 640 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 656 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 658 " --> pdb=" O   GLN A 654 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   PHE A 659 " --> pdb=" O   ILE A 655 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   LYS A 660 " --> pdb=" O   VAL A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 674
      removed outlier: 4.903A  pdb=" N   TYR A 671 " --> pdb=" O   ARG A 667 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TRP A 672 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 701
    Processing helix  chain 'A' and resid 723 through 749
      removed outlier: 5.467A  pdb=" N   LEU A 734 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ASP A 735 " --> pdb=" O   ASN A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 783
      removed outlier: 3.877A  pdb=" N   PHE A 761 " --> pdb=" O   ASN A 757 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 818
      removed outlier: 4.449A  pdb=" N   LEU A 793 " --> pdb=" O   THR A 789 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A 808 " --> pdb=" O   SER A 804 " (cutoff:3.500A)
      Proline residue:  A 810  - end of helix
    Processing helix  chain 'A' and resid 819 through 822
    Processing helix  chain 'A' and resid 823 through 828
    Processing helix  chain 'B' and resid 571 through 598
      removed outlier: 3.889A  pdb=" N   LEU B 577 " --> pdb=" O   VAL B 573 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 609 through 625
      removed outlier: 3.853A  pdb=" N   CYS B 613 " --> pdb=" O   GLY B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 629
    Processing helix  chain 'B' and resid 634 through 666
      removed outlier: 4.950A  pdb=" N   GLN B 642 " --> pdb=" O   CYS B 638 " (cutoff:3.500A)
      Proline residue:  B 643  - end of helix
      Proline residue:  B 648  - end of helix
      removed outlier: 4.448A  pdb=" N   THR B 655 " --> pdb=" O   GLY B 651 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU B 656 " --> pdb=" O   CYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 678
    Processing helix  chain 'B' and resid 679 through 682
      removed outlier: 3.827A  pdb=" N   ARG B 682 " --> pdb=" O   SER B 679 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 679 through 682'
    Processing helix  chain 'B' and resid 683 through 708
      removed outlier: 3.545A  pdb=" N   ILE B 706 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 754
      removed outlier: 3.551A  pdb=" N   LEU B 735 " --> pdb=" O   SER B 731 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY B 736 " --> pdb=" O   TRP B 732 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   LEU B 737 " --> pdb=" O   VAL B 733 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   VAL B 738 " --> pdb=" O   SER B 734 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   HIS B 739 " --> pdb=" O   LEU B 735 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   THR B 741 " --> pdb=" O   LEU B 737 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ASN B 742 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR B 753 " --> pdb=" O   CYS B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 764 through 790
      removed outlier: 4.329A  pdb=" N   GLY B 768 " --> pdb=" O   ASN B 764 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL B 784 " --> pdb=" O   TRP B 780 " (cutoff:3.500A)
      Proline residue:  B 785  - end of helix
    Processing helix  chain 'B' and resid 791 through 793
      No H-bonds generated for 'chain 'B' and resid 791 through 793'
    Processing helix  chain 'B' and resid 794 through 814
      removed outlier: 3.611A  pdb=" N   THR B 813 " --> pdb=" O   GLY B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 814 through 825
      removed outlier: 4.138A  pdb=" N   LYS B 818 " --> pdb=" O   PHE B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 826 through 829
    Processing helix  chain 'B' and resid 830 through 835
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
      removed outlier: 6.258A  pdb=" N   GLN A 555 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   VAL A 718 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 563 through 565
      removed outlier: 3.564A  pdb=" N   GLU B 711 " --> pdb=" O   HIS B 728 " (cutoff:3.500A)

    310 hydrogen bonds defined for protein.
    918 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: 0.59

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1280
        1.35 -     1.46: 1115
        1.46 -     1.58: 2007
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 4456
  Sorted by residual:
  bond pdb=" N   ARG A 554 "
       pdb=" CA  ARG A 554 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" C   LEU B 816 "
       pdb=" O   LEU B 816 "
    ideal  model  delta    sigma   weight residual
    1.244  1.235  0.008 9.80e-03 1.04e+04 7.46e-01
  bond pdb=" C   TYR B 763 "
       pdb=" N   ASN B 764 "
    ideal  model  delta    sigma   weight residual
    1.333  1.344 -0.011 1.30e-02 5.92e+03 7.27e-01
  bond pdb=" C   LEU B 647 "
       pdb=" O   LEU B 647 "
    ideal  model  delta    sigma   weight residual
    1.238  1.248 -0.010 1.28e-02 6.10e+03 5.95e-01
  bond pdb=" N   LEU B 816 "
       pdb=" CA  LEU B 816 "
    ideal  model  delta    sigma   weight residual
    1.459  1.451  0.008 1.04e-02 9.25e+03 5.86e-01
  ... (remaining 4451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 5792
        1.14 -     2.29: 243
        2.29 -     3.43: 52
        3.43 -     4.57: 9
        4.57 -     5.71: 3
  Bond angle restraints: 6099
  Sorted by residual:
  angle pdb=" N   VAL A 620 "
        pdb=" CA  VAL A 620 "
        pdb=" C   VAL A 620 "
      ideal   model   delta    sigma   weight residual
     112.35  108.61    3.74 1.41e+00 5.03e-01 7.05e+00
  angle pdb=" C   HIS B 815 "
        pdb=" N   LEU B 816 "
        pdb=" CA  LEU B 816 "
      ideal   model   delta    sigma   weight residual
     120.09  122.42   -2.33 1.25e+00 6.40e-01 3.48e+00
  angle pdb=" N   PHE B 612 "
        pdb=" CA  PHE B 612 "
        pdb=" CB  PHE B 612 "
      ideal   model   delta    sigma   weight residual
     110.01  107.50    2.51 1.45e+00 4.76e-01 2.99e+00
  angle pdb=" C   LEU B 647 "
        pdb=" CA  LEU B 647 "
        pdb=" CB  LEU B 647 "
      ideal   model   delta    sigma   weight residual
     110.17  113.47   -3.30 1.97e+00 2.58e-01 2.81e+00
  angle pdb=" N   ALA A 782 "
        pdb=" CA  ALA A 782 "
        pdb=" C   ALA A 782 "
      ideal   model   delta    sigma   weight residual
     113.02  115.48   -2.46 1.49e+00 4.50e-01 2.74e+00
  ... (remaining 6094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 2451
       17.25 -    34.50: 116
       34.50 -    51.74: 15
       51.74 -    68.99: 4
       68.99 -    86.24: 1
  Dihedral angle restraints: 2587
    sinusoidal: 965
      harmonic: 1622
  Sorted by residual:
  dihedral pdb=" CA  PRO A 753 "
           pdb=" C   PRO A 753 "
           pdb=" N   THR A 754 "
           pdb=" CA  THR A 754 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.91  -24.09     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ALA A 635 "
           pdb=" C   ALA A 635 "
           pdb=" N   LEU A 636 "
           pdb=" CA  LEU A 636 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.99  -20.01     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  VAL A 617 "
           pdb=" C   VAL A 617 "
           pdb=" N   VAL A 618 "
           pdb=" CA  VAL A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 2584 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 464
       0.027 -    0.055: 157
       0.055 -    0.082: 69
       0.082 -    0.109: 32
       0.109 -    0.137: 6
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  PRO A 594 "
            pdb=" N   PRO A 594 "
            pdb=" C   PRO A 594 "
            pdb=" CB  PRO A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  VAL B 723 "
            pdb=" N   VAL B 723 "
            pdb=" C   VAL B 723 "
            pdb=" CB  VAL B 723 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  VAL B 712 "
            pdb=" N   VAL B 712 "
            pdb=" C   VAL B 712 "
            pdb=" CB  VAL B 712 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 725 not shown)

  Planarity restraints: 737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 805 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   LEU A 805 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 805 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A 806 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 593 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 594 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 594 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 594 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 669 "   -0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO B 670 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 670 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 670 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 734 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1567
        2.87 -     3.38: 4511
        3.38 -     3.89: 6961
        3.89 -     4.39: 7810
        4.39 -     4.90: 13102
  Nonbonded interactions: 33951
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 626 "
            pdb=" OG1 THR A 629 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" N   LYS A 626 "
            pdb=" OG1 THR A 629 "
     model   vdw
     2.462 3.120
  nonbonded pdb=" O   SER B 731 "
            pdb=" OG  SER B 734 "
     model   vdw
     2.473 3.040
  nonbonded pdb=" N   GLU B 832 "
            pdb=" OE1 GLU B 832 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" O   ILE A 643 "
            pdb=" OG  SER A 646 "
     model   vdw
     2.500 3.040
  ... (remaining 33946 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     5.260
  Find NCS groups from input model:        0.010
  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:0.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4456  Z= 0.145
  Angle     :  0.581   5.715   6099  Z= 0.321
  Chirality :  0.037   0.137    728
  Planarity :  0.005   0.034    737
  Dihedral  : 10.912  86.238   1537
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 0.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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:  0.71 (0.36), residues: 549
  helix:  1.08 (0.25), residues: 390
  sheet: -1.21 (0.96), residues: 24
  loop : -0.80 (0.60), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 707 
 TYR   0.009   0.001   TYR A 669 
 PHE   0.018   0.001   PHE B 612 
 TRP   0.011   0.001   TRP B 685 
 HIS   0.005   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4456)
  covalent geometry    : angle       0.58130 ( 6099)
  hydrogen bonds       : bond        0.10118 (  310)
  hydrogen bonds       : angle       6.01208 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  554 ARG cc_start: 0.6247 (mtm180) cc_final: 0.4728 (ptp-170)
REVERT: A  660 LYS cc_start: 0.7078 (mttt) cc_final: 0.6854 (mtmm)
REVERT: A  664 ARG cc_start: 0.6479 (ttt180) cc_final: 0.6119 (ttm-80)
REVERT: A  682 MET cc_start: 0.7348 (mtm) cc_final: 0.7112 (mtp)
REVERT: B  562 ARG cc_start: 0.6933 (mtt-85) cc_final: 0.4096 (ptt-90)
REVERT: B  565 LYS cc_start: 0.8387 (tttt) cc_final: 0.8180 (tttp)
REVERT: B  789 ASN cc_start: 0.7841 (m-40) cc_final: 0.7603 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0747
  time to fit residues: 10.8548
Evaluate side-chains
  83 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.163466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.134970 restraints weight = 5707.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137254 restraints weight = 3845.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139080 restraints weight = 3060.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139854 restraints weight = 2660.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139854 restraints weight = 2447.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4456  Z= 0.155
  Angle     :  0.599   6.191   6099  Z= 0.314
  Chirality :  0.041   0.150    728
  Planarity :  0.005   0.043    737
  Dihedral  :  4.684  19.732    591
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  :  7.11 %
    Favored  : 89.12 %
  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:  1.53 (0.37), residues: 549
  helix:  1.71 (0.26), residues: 414
  sheet: -1.03 (0.74), residues: 37
  loop : -1.05 (0.63), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 667 
 TYR   0.012   0.001   TYR A 783 
 PHE   0.024   0.002   PHE A 684 
 TRP   0.006   0.001   TRP B 685 
 HIS   0.003   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4456)
  covalent geometry    : angle       0.59892 ( 6099)
  hydrogen bonds       : bond        0.04497 (  310)
  hydrogen bonds       : angle       4.51372 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  755 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7774 (m-40)
REVERT: A  766 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8585 (mmt)
REVERT: B  562 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.4419 (ptt-90)
REVERT: B  669 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0541
  time to fit residues: 6.3746
Evaluate side-chains
  92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:    0.3980
   chunk 41 optimal weight:    0.0470
   chunk 52 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A 828 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.165082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.136446 restraints weight = 5568.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138816 restraints weight = 3656.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141022 restraints weight = 2849.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141805 restraints weight = 2430.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141805 restraints weight = 2235.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4456  Z= 0.116
  Angle     :  0.537   6.690   6099  Z= 0.276
  Chirality :  0.039   0.130    728
  Planarity :  0.004   0.045    737
  Dihedral  :  4.285  19.284    591
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 10.04 %
    Favored  : 86.61 %
  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:  2.04 (0.37), residues: 549
  helix:  2.11 (0.26), residues: 411
  sheet: -0.68 (0.78), residues: 37
  loop : -1.01 (0.62), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 651 
 TYR   0.008   0.001   TYR A 783 
 PHE   0.025   0.001   PHE A 684 
 TRP   0.008   0.001   TRP B 716 
 HIS   0.003   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4456)
  covalent geometry    : angle       0.53698 ( 6099)
  hydrogen bonds       : bond        0.03803 (  310)
  hydrogen bonds       : angle       4.21519 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  682 MET cc_start: 0.7071 (mtm) cc_final: 0.6789 (mtm)
REVERT: A  755 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7971 (m-40)
REVERT: B  562 ARG cc_start: 0.7608 (mtt-85) cc_final: 0.4519 (ptt-90)
REVERT: B  669 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8619 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0647
  time to fit residues: 7.1585
Evaluate side-chains
  91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  706 ILE
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  816 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 634 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.164891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.136493 restraints weight = 5546.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.139072 restraints weight = 3637.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140863 restraints weight = 2851.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141716 restraints weight = 2449.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142574 restraints weight = 2247.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4456  Z= 0.119
  Angle     :  0.538   7.023   6099  Z= 0.273
  Chirality :  0.038   0.132    728
  Planarity :  0.004   0.047    737
  Dihedral  :  4.192  18.638    591
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 11.30 %
    Favored  : 84.31 %
  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:  2.22 (0.37), residues: 549
  helix:  2.22 (0.26), residues: 412
  sheet: -0.58 (0.79), residues: 37
  loop : -0.90 (0.62), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 651 
 TYR   0.008   0.001   TYR B 776 
 PHE   0.026   0.001   PHE A 684 
 TRP   0.007   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4456)
  covalent geometry    : angle       0.53783 ( 6099)
  hydrogen bonds       : bond        0.03718 (  310)
  hydrogen bonds       : angle       4.07353 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  755 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7799 (m-40)
REVERT: A  766 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8632 (mmm)
REVERT: B  562 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.4503 (ptp90)
REVERT: B  669 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8596 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0677
  time to fit residues: 7.7311
Evaluate side-chains
  95 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0270
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A 590 HIS
A 634 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.165863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.138866 restraints weight = 5583.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.139829 restraints weight = 3962.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.139825 restraints weight = 3351.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140120 restraints weight = 3371.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.140320 restraints weight = 3136.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4456  Z= 0.111
  Angle     :  0.541   7.099   6099  Z= 0.275
  Chirality :  0.038   0.132    728
  Planarity :  0.004   0.047    737
  Dihedral  :  4.127  18.398    591
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.18 %
    Favored  : 83.47 %
  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:  2.34 (0.37), residues: 549
  helix:  2.27 (0.26), residues: 414
  sheet: -0.77 (0.79), residues: 37
  loop : -0.67 (0.65), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 667 
 TYR   0.008   0.001   TYR B 776 
 PHE   0.026   0.001   PHE A 684 
 TRP   0.009   0.001   TRP B 716 
 HIS   0.002   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4456)
  covalent geometry    : angle       0.54070 ( 6099)
  hydrogen bonds       : bond        0.03507 (  310)
  hydrogen bonds       : angle       3.99439 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  651 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7039 (mtp85)
REVERT: A  661 MET cc_start: 0.8251 (mmm) cc_final: 0.8019 (mmp)
REVERT: A  766 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8686 (mmm)
REVERT: B  562 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.4370 (ptp90)
REVERT: B  669 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0661
  time to fit residues: 7.3617
Evaluate side-chains
  91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0010
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 755 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.165666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137176 restraints weight = 5689.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139710 restraints weight = 3825.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.141215 restraints weight = 3033.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141800 restraints weight = 2654.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.142558 restraints weight = 2475.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4456  Z= 0.117
  Angle     :  0.548   7.747   6099  Z= 0.277
  Chirality :  0.038   0.128    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.085  17.409    591
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.60 %
    Favored  : 82.64 %
  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:  2.38 (0.37), residues: 549
  helix:  2.30 (0.26), residues: 414
  sheet: -0.90 (0.78), residues: 37
  loop : -0.58 (0.65), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 651 
 TYR   0.008   0.001   TYR B 776 
 PHE   0.028   0.001   PHE A 684 
 TRP   0.008   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4456)
  covalent geometry    : angle       0.54754 ( 6099)
  hydrogen bonds       : bond        0.03511 (  310)
  hydrogen bonds       : angle       3.94715 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  651 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7184 (mtp85)
REVERT: A  661 MET cc_start: 0.8230 (mmm) cc_final: 0.7886 (mmp)
REVERT: A  697 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6310 (ptt)
REVERT: A  766 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8671 (mmm)
REVERT: B  562 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.4507 (ptp90)
REVERT: B  669 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8600 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0728
  time to fit residues: 7.7490
Evaluate side-chains
  94 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  669 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.3678

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

Flipped N/Q/H residues before XYZ refinement:
A 634 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.166508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138064 restraints weight = 5669.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140489 restraints weight = 3852.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.142114 restraints weight = 3044.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143174 restraints weight = 2660.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143174 restraints weight = 2417.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4456  Z= 0.109
  Angle     :  0.551  11.472   6099  Z= 0.276
  Chirality :  0.038   0.125    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.032  17.965    591
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.85 %
    Favored  : 81.59 %
  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:  2.48 (0.37), residues: 549
  helix:  2.37 (0.26), residues: 413
  sheet: -0.93 (0.78), residues: 37
  loop : -0.46 (0.65), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 667 
 TYR   0.008   0.001   TYR B 776 
 PHE   0.027   0.001   PHE A 684 
 TRP   0.008   0.001   TRP B 716 
 HIS   0.003   0.001   HIS A 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4456)
  covalent geometry    : angle       0.55076 ( 6099)
  hydrogen bonds       : bond        0.03401 (  310)
  hydrogen bonds       : angle       3.93996 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.6678 (m-70) cc_final: 0.6471 (m90)
REVERT: A  766 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8593 (mmm)
REVERT: B  562 ARG cc_start: 0.7746 (mtt-85) cc_final: 0.4497 (ptp90)
  outliers start: 17
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0770
  time to fit residues: 8.2415
Evaluate side-chains
  93 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0570
   chunk 46 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 755 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.164415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.135472 restraints weight = 5658.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138046 restraints weight = 3798.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.139483 restraints weight = 2987.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.140826 restraints weight = 2593.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141332 restraints weight = 2364.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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   0.036   4456  Z= 0.137
  Angle     :  0.595  10.946   6099  Z= 0.295
  Chirality :  0.039   0.134    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.107  17.661    591
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.44 %
    Favored  : 82.01 %
  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:  2.39 (0.37), residues: 549
  helix:  2.33 (0.26), residues: 413
  sheet: -0.87 (0.80), residues: 37
  loop : -0.66 (0.65), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 667 
 TYR   0.009   0.001   TYR A 756 
 PHE   0.028   0.001   PHE A 684 
 TRP   0.005   0.001   TRP B 716 
 HIS   0.003   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4456)
  covalent geometry    : angle       0.59512 ( 6099)
  hydrogen bonds       : bond        0.03668 (  310)
  hydrogen bonds       : angle       4.00990 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  651 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7175 (mtp85)
REVERT: A  667 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8291 (ttm110)
REVERT: A  766 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8681 (mmm)
REVERT: B  562 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7399 (mtt90)
  outliers start: 17
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0738
  time to fit residues: 7.7534
Evaluate side-chains
  92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0170
   chunk 1 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A 634 GLN
A 755 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.166156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137803 restraints weight = 5682.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.140184 restraints weight = 3853.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141849 restraints weight = 3042.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.143003 restraints weight = 2610.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143240 restraints weight = 2380.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4456  Z= 0.112
  Angle     :  0.582  12.655   6099  Z= 0.288
  Chirality :  0.038   0.124    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.029  18.533    591
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.48 %
    Favored  : 81.38 %
  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:  2.52 (0.37), residues: 549
  helix:  2.39 (0.26), residues: 412
  sheet: -0.88 (0.82), residues: 37
  loop : -0.37 (0.67), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 667 
 TYR   0.008   0.001   TYR A 756 
 PHE   0.028   0.001   PHE A 684 
 TRP   0.008   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4456)
  covalent geometry    : angle       0.58161 ( 6099)
  hydrogen bonds       : bond        0.03420 (  310)
  hydrogen bonds       : angle       3.95525 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  659 PHE cc_start: 0.6953 (t80) cc_final: 0.6723 (t80)
REVERT: A  766 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8589 (mmm)
REVERT: B  562 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.4421 (ptp90)
REVERT: B  704 TYR cc_start: 0.7945 (t80) cc_final: 0.7736 (t80)
  outliers start: 15
  outliers final: 14
  residues processed: 83
  average time/residue: 0.0752
  time to fit residues: 7.6410
Evaluate side-chains
  90 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  755 ASN
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0670
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.166051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137672 restraints weight = 5633.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.140115 restraints weight = 3854.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141818 restraints weight = 3057.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.142632 restraints weight = 2653.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143373 restraints weight = 2443.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4456  Z= 0.117
  Angle     :  0.587  12.328   6099  Z= 0.290
  Chirality :  0.038   0.125    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.046  17.683    591
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.11 %
    Favored  : 80.75 %
  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:  2.51 (0.37), residues: 549
  helix:  2.39 (0.26), residues: 414
  sheet: -0.89 (0.85), residues: 37
  loop : -0.49 (0.67), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 651 
 TYR   0.008   0.001   TYR B 776 
 PHE   0.029   0.001   PHE A 684 
 TRP   0.007   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4456)
  covalent geometry    : angle       0.58723 ( 6099)
  hydrogen bonds       : bond        0.03443 (  310)
  hydrogen bonds       : angle       4.03154 (  918)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  659 PHE cc_start: 0.6968 (t80) cc_final: 0.6732 (t80)
REVERT: A  766 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8586 (mmm)
REVERT: B  562 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7320 (mtt90)
  outliers start: 15
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0610
  time to fit residues: 6.2674
Evaluate side-chains
  88 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  812 CYS
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  790 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 634 GLN
A 755 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.165214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.136175 restraints weight = 5697.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138905 restraints weight = 3708.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140646 restraints weight = 2870.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141783 restraints weight = 2451.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141783 restraints weight = 2222.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4456  Z= 0.122
  Angle     :  0.596  12.070   6099  Z= 0.295
  Chirality :  0.038   0.127    728
  Planarity :  0.004   0.046    737
  Dihedral  :  4.044  18.242    591
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.53 %
    Favored  : 80.33 %
  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:  2.60 (0.37), residues: 549
  helix:  2.48 (0.26), residues: 407
  sheet: -0.84 (0.86), residues: 37
  loop : -0.35 (0.63), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 651 
 TYR   0.013   0.001   TYR B 704 
 PHE   0.029   0.001   PHE A 684 
 TRP   0.006   0.001   TRP B 732 
 HIS   0.003   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4456)
  covalent geometry    : angle       0.59559 ( 6099)
  hydrogen bonds       : bond        0.03483 (  310)
  hydrogen bonds       : angle       4.02248 (  918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 802.09 seconds
wall clock time: 14 minutes 27.42 seconds (867.42 seconds total)