Starting phenix.real_space_refine
on Wed Sep 17 05:13:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uta_64486/09_2025/9uta_64486.cif"
  }
  resolution = 3.77
  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=   0.008
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      45      5.16       5
     C    3096      2.51       5
     N     764      2.21       5
     O     796      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4701
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2487
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 19, 'TRANS': 296}
    Chain: "B"
      Number of atoms: 2214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2214
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 19, 'TRANS': 266}
  Time building chain proxies: 1.40, per 1000 atoms: 0.30
  Number of scatterers: 4701
  At special positions: 0
  Unit cell: (71.04, 86.4, 107.52, 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      45     16.00
     O     796      8.00
     N     764      7.00
     C    3096      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 551 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 720 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 541 " - pdb=" SG  CYS B 554 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 633 " - pdb=" SG  CYS B 722 " distance=2.23

  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: 0.43
  Conformation dependent library (CDL) restraints added in 187.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1138

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      72.1% alpha, 4.2% 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 589
      removed outlier: 3.686A  pdb=" N   GLY A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.654A  pdb=" N   ALA A 599 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 618
      removed outlier: 4.033A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 610 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL A 613 " --> pdb=" O   THR A 609 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL A 618 " --> pdb=" O   ALA A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 621
      No H-bonds generated for 'chain 'A' and resid 619 through 621'
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.160A  pdb=" N   CYS A 632 " --> pdb=" O   SER A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 665
      removed outlier: 3.867A  pdb=" N   CYS A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE A 641 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   THR A 642 " --> pdb=" O   PRO A 638 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ILE A 648 " --> pdb=" O   CYS A 644 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   PHE A 659 " --> pdb=" O   ILE A 655 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A 662 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 676
      removed outlier: 3.536A  pdb=" N   ARG A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   TYR A 675 " --> pdb=" O   TYR A 671 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLN A 676 " --> pdb=" O   TRP A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 700
      removed outlier: 4.165A  pdb=" N   SER A 681 " --> pdb=" O   GLY A 677 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE A 685 " --> pdb=" O   SER A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 723
    Processing helix  chain 'A' and resid 724 through 730
    Processing helix  chain 'A' and resid 733 through 749
    Processing helix  chain 'A' and resid 758 through 783
      removed outlier: 3.996A  pdb=" N   ALA A 782 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 805
      removed outlier: 3.921A  pdb=" N   ILE A 803 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 818
    Processing helix  chain 'A' and resid 823 through 833
      removed outlier: 4.316A  pdb=" N   GLN A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   GLY A 833 " --> pdb=" O   SER A 829 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 593
    Processing helix  chain 'B' and resid 596 through 603
    Processing helix  chain 'B' and resid 604 through 620
    Processing helix  chain 'B' and resid 621 through 623
      No H-bonds generated for 'chain 'B' and resid 621 through 623'
    Processing helix  chain 'B' and resid 629 through 635
    Processing helix  chain 'B' and resid 637 through 663
      Proline residue:  B 643  - end of helix
      removed outlier: 5.176A  pdb=" N   THR B 650 " --> pdb=" O   GLY B 646 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B 651 " --> pdb=" O   CYS B 647 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLU B 661 " --> pdb=" O   GLU B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 677
      removed outlier: 3.627A  pdb=" N   ARG B 677 " --> pdb=" O   SER B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 703
    Processing helix  chain 'B' and resid 727 through 749
      removed outlier: 5.280A  pdb=" N   THR B 736 " --> pdb=" O   LEU B 732 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   ASN B 737 " --> pdb=" O   ALA B 733 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 784
      removed outlier: 4.500A  pdb=" N   GLY B 763 " --> pdb=" O   ASN B 759 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU B 764 " --> pdb=" O   ARG B 760 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA B 770 " --> pdb=" O   PHE B 766 " (cutoff:3.500A)
      Proline residue:  B 780  - end of helix
    Processing helix  chain 'B' and resid 790 through 806
      removed outlier: 3.985A  pdb=" N   GLN B 794 " --> pdb=" O   ARG B 790 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   MET B 795 " --> pdb=" O   PRO B 791 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY B 796 " --> pdb=" O   ALA B 792 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 798 " --> pdb=" O   GLN B 794 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 799 " --> pdb=" O   MET B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 824
      removed outlier: 4.116A  pdb=" N   ARG B 813 " --> pdb=" O   PHE B 809 " (cutoff:3.500A)
      Proline residue:  B 821  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
      removed outlier: 3.930A  pdb=" N   VAL A 718 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 558 through 560
      removed outlier: 6.320A  pdb=" N   ARG B 558 " --> pdb=" O   ALA B 718 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL B 720 " --> pdb=" O   ARG B 558 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ARG B 560 " --> pdb=" O   VAL B 720 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   CYS B 722 " --> pdb=" O   ARG B 560 " (cutoff:3.500A)
      removed outlier: 9.109A  pdb=" N   GLU B 717 " --> pdb=" O   HIS B 712 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   HIS B 712 " --> pdb=" O   GLU B 717 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU B 706 " --> pdb=" O   ARG B 723 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    870 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: 0.69

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1436
        1.34 -     1.46: 1204
        1.46 -     1.58: 2132
        1.58 -     1.70: 0
        1.70 -     1.82: 62
  Bond restraints: 4834
  Sorted by residual:
  bond pdb=" CA  LEU B 806 "
       pdb=" C   LEU B 806 "
    ideal  model  delta    sigma   weight residual
    1.522  1.471  0.050 1.72e-02 3.38e+03 8.55e+00
  bond pdb=" C   PHE B 778 "
       pdb=" N   VAL B 779 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.13e-02 7.83e+03 3.44e+00
  bond pdb=" N   PRO B 791 "
       pdb=" CA  PRO B 791 "
    ideal  model  delta    sigma   weight residual
    1.469  1.445  0.023 1.28e-02 6.10e+03 3.29e+00
  bond pdb=" CB  PRO B 791 "
       pdb=" CG  PRO B 791 "
    ideal  model  delta    sigma   weight residual
    1.492  1.580 -0.088 5.00e-02 4.00e+02 3.09e+00
  bond pdb=" C   ILE B 805 "
       pdb=" N   LEU B 806 "
    ideal  model  delta    sigma   weight residual
    1.333  1.307  0.026 1.56e-02 4.11e+03 2.84e+00
  ... (remaining 4829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 6515
        2.50 -     5.01: 84
        5.01 -     7.51: 7
        7.51 -    10.01: 0
       10.01 -    12.51: 1
  Bond angle restraints: 6607
  Sorted by residual:
  angle pdb=" CA  PRO B 791 "
        pdb=" N   PRO B 791 "
        pdb=" CD  PRO B 791 "
      ideal   model   delta    sigma   weight residual
     112.00   99.49   12.51 1.40e+00 5.10e-01 7.99e+01
  angle pdb=" CA  PRO A 638 "
        pdb=" N   PRO A 638 "
        pdb=" CD  PRO A 638 "
      ideal   model   delta    sigma   weight residual
     112.00  105.14    6.86 1.40e+00 5.10e-01 2.40e+01
  angle pdb=" N   VAL B 793 "
        pdb=" CA  VAL B 793 "
        pdb=" C   VAL B 793 "
      ideal   model   delta    sigma   weight residual
     111.67  108.66    3.01 9.50e-01 1.11e+00 1.00e+01
  angle pdb=" N   PHE B 778 "
        pdb=" CA  PHE B 778 "
        pdb=" CB  PHE B 778 "
      ideal   model   delta    sigma   weight residual
     110.30  114.15   -3.85 1.54e+00 4.22e-01 6.26e+00
  angle pdb=" C   SER B 777 "
        pdb=" N   PHE B 778 "
        pdb=" CA  PHE B 778 "
      ideal   model   delta    sigma   weight residual
     120.68  116.46    4.22 1.70e+00 3.46e-01 6.17e+00
  ... (remaining 6602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2464
       17.98 -    35.96: 289
       35.96 -    53.94: 70
       53.94 -    71.91: 22
       71.91 -    89.89: 3
  Dihedral angle restraints: 2848
    sinusoidal: 1089
      harmonic: 1759
  Sorted by residual:
  dihedral pdb=" CB  CYS B 633 "
           pdb=" SG  CYS B 633 "
           pdb=" SG  CYS B 722 "
           pdb=" CB  CYS B 722 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.28   60.72     1      1.00e+01 1.00e-02 4.90e+01
  dihedral pdb=" CA  ALA B 735 "
           pdb=" C   ALA B 735 "
           pdb=" N   THR B 736 "
           pdb=" CA  THR B 736 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  SER A 547 "
           pdb=" C   SER A 547 "
           pdb=" N   GLU A 548 "
           pdb=" CA  GLU A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.45   16.55     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 2845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 466
       0.029 -    0.058: 208
       0.058 -    0.088: 73
       0.088 -    0.117: 23
       0.117 -    0.146: 8
  Chirality restraints: 778
  Sorted by residual:
  chirality pdb=" CB  VAL A 786 "
            pdb=" CA  VAL A 786 "
            pdb=" CG1 VAL A 786 "
            pdb=" CG2 VAL A 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  PRO B 791 "
            pdb=" N   PRO B 791 "
            pdb=" C   PRO B 791 "
            pdb=" CB  PRO B 791 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  ILE A 518 "
            pdb=" N   ILE A 518 "
            pdb=" C   ILE A 518 "
            pdb=" CB  ILE A 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 775 not shown)

  Planarity restraints: 815
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 790 "   -0.098 5.00e-02 4.00e+02   1.38e-01 3.05e+01
        pdb=" N   PRO B 791 "    0.238 5.00e-02 4.00e+02
        pdb=" CA  PRO B 791 "   -0.067 5.00e-02 4.00e+02
        pdb=" CD  PRO B 791 "   -0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 637 "    0.057 5.00e-02 4.00e+02   8.20e-02 1.08e+01
        pdb=" N   PRO A 638 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 823 "   -0.047 5.00e-02 4.00e+02   7.13e-02 8.14e+00
        pdb=" N   PRO A 824 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 824 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 824 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 812 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 462
        2.73 -     3.27: 5163
        3.27 -     3.81: 7877
        3.81 -     4.36: 8658
        4.36 -     4.90: 14271
  Nonbonded interactions: 36431
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 760 "
            pdb=" OG1 THR A 763 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   PRO A 638 "
            pdb=" NZ  LYS A 689 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   PHE A 659 "
            pdb=" OG  SER A 663 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE1 GLU A 560 "
            pdb=" N   TRP A 561 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   PRO B 548 "
            pdb=" OG  SER B 551 "
     model   vdw
     2.317 3.040
  ... (remaining 36426 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:             3.790
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.160
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
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      :  0.006   0.197   4839  Z= 0.292
  Angle     :  0.831  25.899   6617  Z= 0.447
  Chirality :  0.040   0.146    778
  Planarity :  0.008   0.138    815
  Dihedral  : 16.779  89.893   1695
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 25.05 %
    Favored  : 74.76 %
  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 aren not related in a simple way.
  whole: -1.45 (0.33), residues: 598
  helix: -0.15 (0.26), residues: 388
  sheet: -1.38 (0.98), residues: 23
  loop : -2.55 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 813 
 TYR   0.016   0.002   TYR A 545 
 PHE   0.023   0.002   PHE B 540 
 TRP   0.010   0.001   TRP B 775 
 HIS   0.009   0.002   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 4834)
  covalent geometry    : angle       0.73416 ( 6607)
  SS BOND              : bond        0.08805 (    5)
  SS BOND              : angle      10.03845 (   10)
  hydrogen bonds       : bond        0.15835 (  292)
  hydrogen bonds       : angle       6.17601 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  552 PHE cc_start: 0.4925 (m-80) cc_final: 0.4049 (m-10)
REVERT: A  733 SER cc_start: 0.8517 (p) cc_final: 0.8198 (p)
REVERT: B  703 PHE cc_start: 0.6992 (m-80) cc_final: 0.6533 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0836
  time to fit residues: 18.5372
Evaluate side-chains
  112 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN
A 592 GLN
A 757 ASN
B 654 GLN
B 734 HIS
B 794 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.136907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.115455 restraints weight = 11377.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.118878 restraints weight = 6197.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.121170 restraints weight = 4050.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.122751 restraints weight = 2994.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.123739 restraints weight = 2409.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4839  Z= 0.152
  Angle     :  0.757  10.488   6617  Z= 0.373
  Chirality :  0.042   0.187    778
  Planarity :  0.007   0.073    815
  Dihedral  :  4.428  15.397    650
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 23.51 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.34), residues: 598
  helix:  0.93 (0.26), residues: 390
  sheet: -0.69 (0.96), residues: 26
  loop : -1.85 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 674 
 TYR   0.019   0.002   TYR B 815 
 PHE   0.012   0.001   PHE B 730 
 TRP   0.010   0.001   TRP B 775 
 HIS   0.006   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4834)
  covalent geometry    : angle       0.75450 ( 6607)
  SS BOND              : bond        0.00363 (    5)
  SS BOND              : angle       1.82162 (   10)
  hydrogen bonds       : bond        0.05019 (  292)
  hydrogen bonds       : angle       4.29807 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.7486 (tp30) cc_final: 0.7069 (tp30)
REVERT: A  552 PHE cc_start: 0.4758 (m-80) cc_final: 0.4236 (m-10)
REVERT: A  633 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7238 (ttt180)
REVERT: A  689 LYS cc_start: 0.8636 (tppt) cc_final: 0.8328 (tptp)
REVERT: A  733 SER cc_start: 0.9100 (p) cc_final: 0.8891 (p)
REVERT: B  703 PHE cc_start: 0.7587 (m-80) cc_final: 0.6230 (t80)
REVERT: B  717 GLU cc_start: 0.7500 (mp0) cc_final: 0.7173 (mp0)
REVERT: B  734 HIS cc_start: 0.5292 (t-90) cc_final: 0.5087 (t-90)
REVERT: B  746 LEU cc_start: 0.8429 (tt) cc_final: 0.7945 (mp)
REVERT: B  768 MET cc_start: 0.9196 (mmp) cc_final: 0.8436 (mmp)
REVERT: B  775 TRP cc_start: 0.7999 (m100) cc_final: 0.7599 (m100)
REVERT: B  790 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7474 (mpt-90)
  outliers start: 30
  outliers final: 16
  residues processed: 135
  average time/residue: 0.0721
  time to fit residues: 12.3159
Evaluate side-chains
  122 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  589 ARG
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain B residue  554 CYS
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  774 THR
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  785 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0010
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0170
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.3824

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
B 593 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.136428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.114385 restraints weight = 11080.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.117723 restraints weight = 6054.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.119953 restraints weight = 4005.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.121403 restraints weight = 2995.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.122541 restraints weight = 2451.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4839  Z= 0.133
  Angle     :  0.691   9.412   6617  Z= 0.338
  Chirality :  0.040   0.125    778
  Planarity :  0.006   0.063    815
  Dihedral  :  4.239  15.112    650
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 25.24 %
    Favored  : 70.33 %
  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 aren not related in a simple way.
  whole:  0.66 (0.35), residues: 598
  helix:  1.40 (0.27), residues: 395
  sheet: -0.25 (1.18), residues: 20
  loop : -1.63 (0.45), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 557 
 TYR   0.020   0.002   TYR B 815 
 PHE   0.012   0.001   PHE A 637 
 TRP   0.009   0.001   TRP B 546 
 HIS   0.008   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4834)
  covalent geometry    : angle       0.68852 ( 6607)
  SS BOND              : bond        0.00350 (    5)
  SS BOND              : angle       1.63112 (   10)
  hydrogen bonds       : bond        0.04292 (  292)
  hydrogen bonds       : angle       3.97732 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.7639 (tp30) cc_final: 0.6941 (tp30)
REVERT: A  616 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7263 (ttm)
REVERT: A  633 ARG cc_start: 0.7584 (ttt180) cc_final: 0.7210 (ttt-90)
REVERT: A  689 LYS cc_start: 0.8795 (tppt) cc_final: 0.8448 (tptp)
REVERT: A  716 THR cc_start: 0.8009 (p) cc_final: 0.7754 (t)
REVERT: A  739 SER cc_start: 0.9201 (t) cc_final: 0.8831 (p)
REVERT: B  545 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: B  703 PHE cc_start: 0.7517 (m-80) cc_final: 0.6123 (t80)
REVERT: B  768 MET cc_start: 0.9251 (mmp) cc_final: 0.8527 (mmp)
REVERT: B  775 TRP cc_start: 0.7541 (m100) cc_final: 0.7236 (m100)
REVERT: B  790 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7923 (tpp80)
  outliers start: 23
  outliers final: 10
  residues processed: 133
  average time/residue: 0.0669
  time to fit residues: 11.4687
Evaluate side-chains
  108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 ASP
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  778 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0870
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.132420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.110346 restraints weight = 11531.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.113652 restraints weight = 6159.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.115837 restraints weight = 4045.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.117213 restraints weight = 3025.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.118226 restraints weight = 2499.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4839  Z= 0.148
  Angle     :  0.729   8.734   6617  Z= 0.352
  Chirality :  0.041   0.119    778
  Planarity :  0.006   0.056    815
  Dihedral  :  4.321  16.552    650
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 25.05 %
    Favored  : 68.02 %
  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 aren not related in a simple way.
  whole:  0.69 (0.35), residues: 598
  helix:  1.35 (0.26), residues: 402
  sheet: -0.44 (1.08), residues: 20
  loop : -1.51 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 553 
 TYR   0.018   0.002   TYR B 815 
 PHE   0.013   0.001   PHE A 637 
 TRP   0.023   0.001   TRP B 680 
 HIS   0.004   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4834)
  covalent geometry    : angle       0.72875 ( 6607)
  SS BOND              : bond        0.00861 (    5)
  SS BOND              : angle       1.07596 (   10)
  hydrogen bonds       : bond        0.04758 (  292)
  hydrogen bonds       : angle       3.93989 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 106
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7322 (ttm)
REVERT: A  633 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7346 (ttt-90)
REVERT: A  674 ARG cc_start: 0.7817 (ptt180) cc_final: 0.7605 (ptt90)
REVERT: A  689 LYS cc_start: 0.8858 (tppt) cc_final: 0.8473 (tptp)
REVERT: A  739 SER cc_start: 0.9224 (t) cc_final: 0.8934 (p)
REVERT: B  545 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7910 (mm-30)
REVERT: B  703 PHE cc_start: 0.7754 (m-80) cc_final: 0.6198 (t80)
REVERT: B  790 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7914 (tpp80)
  outliers start: 36
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0623
  time to fit residues: 10.3048
Evaluate side-chains
  122 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  774 THR
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.131377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.109482 restraints weight = 11838.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.112620 restraints weight = 6479.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.114750 restraints weight = 4310.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.116055 restraints weight = 3252.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.117066 restraints weight = 2698.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.6596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4839  Z= 0.149
  Angle     :  0.729   7.907   6617  Z= 0.355
  Chirality :  0.040   0.206    778
  Planarity :  0.006   0.050    815
  Dihedral  :  4.313  18.347    650
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 24.28 %
    Favored  : 68.40 %
  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 aren not related in a simple way.
  whole:  0.72 (0.35), residues: 598
  helix:  1.35 (0.26), residues: 404
  sheet: -0.75 (1.04), residues: 22
  loop : -1.43 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 821 
 TYR   0.017   0.002   TYR B 815 
 PHE   0.017   0.001   PHE A 637 
 TRP   0.034   0.002   TRP B 680 
 HIS   0.003   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4834)
  covalent geometry    : angle       0.72869 ( 6607)
  SS BOND              : bond        0.00448 (    5)
  SS BOND              : angle       1.04789 (   10)
  hydrogen bonds       : bond        0.04620 (  292)
  hydrogen bonds       : angle       3.99290 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.8288 (tp30) cc_final: 0.7571 (tp30)
REVERT: A  616 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7347 (ttm)
REVERT: A  672 TRP cc_start: 0.6790 (OUTLIER) cc_final: 0.6456 (t-100)
REVERT: A  689 LYS cc_start: 0.8924 (tppt) cc_final: 0.8525 (tptp)
REVERT: A  739 SER cc_start: 0.9249 (t) cc_final: 0.8996 (p)
REVERT: B  545 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8160 (mm-30)
REVERT: B  555 PHE cc_start: 0.7604 (t80) cc_final: 0.7320 (t80)
REVERT: B  703 PHE cc_start: 0.7783 (m-80) cc_final: 0.6190 (t80)
REVERT: B  752 ARG cc_start: 0.7446 (ptm160) cc_final: 0.7068 (ptm160)
REVERT: B  768 MET cc_start: 0.9146 (mmp) cc_final: 0.8510 (mmp)
  outliers start: 38
  outliers final: 28
  residues processed: 122
  average time/residue: 0.0575
  time to fit residues: 9.4362
Evaluate side-chains
  122 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  774 THR
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Chi-restraints excluded: chain B residue  800 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0030
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4108

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.133574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.111321 restraints weight = 11998.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.114606 restraints weight = 6518.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.116791 restraints weight = 4296.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.118249 restraints weight = 3221.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119016 restraints weight = 2634.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.6959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4839  Z= 0.127
  Angle     :  0.717   9.463   6617  Z= 0.343
  Chirality :  0.039   0.172    778
  Planarity :  0.006   0.047    815
  Dihedral  :  4.115  17.110    650
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 28.52 %
    Favored  : 66.67 %
  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 aren not related in a simple way.
  whole:  0.94 (0.35), residues: 598
  helix:  1.55 (0.26), residues: 404
  sheet: -1.16 (1.14), residues: 18
  loop : -1.37 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 557 
 TYR   0.016   0.001   TYR A 724 
 PHE   0.019   0.001   PHE A 637 
 TRP   0.009   0.001   TRP B 775 
 HIS   0.005   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4834)
  covalent geometry    : angle       0.71651 ( 6607)
  SS BOND              : bond        0.00440 (    5)
  SS BOND              : angle       0.93037 (   10)
  hydrogen bonds       : bond        0.04053 (  292)
  hydrogen bonds       : angle       3.86518 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.8317 (tp30) cc_final: 0.8026 (tp30)
REVERT: A  689 LYS cc_start: 0.8904 (tppt) cc_final: 0.8527 (tptp)
REVERT: A  739 SER cc_start: 0.9329 (t) cc_final: 0.9022 (p)
REVERT: B  703 PHE cc_start: 0.7871 (m-80) cc_final: 0.6238 (t80)
REVERT: B  752 ARG cc_start: 0.7383 (ptm160) cc_final: 0.6979 (ptm160)
REVERT: B  768 MET cc_start: 0.9203 (mmp) cc_final: 0.8630 (mmp)
  outliers start: 25
  outliers final: 20
  residues processed: 113
  average time/residue: 0.0593
  time to fit residues: 9.0974
Evaluate side-chains
  111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  711 TRP
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
A 676 GLN
B 593 HIS
B 721 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.128556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.106798 restraints weight = 11863.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.109884 restraints weight = 6491.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.111922 restraints weight = 4309.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.113289 restraints weight = 3250.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.114011 restraints weight = 2675.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.7235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4839  Z= 0.165
  Angle     :  0.750   9.056   6617  Z= 0.367
  Chirality :  0.041   0.163    778
  Planarity :  0.006   0.049    815
  Dihedral  :  4.378  18.832    650
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  8.29 %
    Allowed  : 25.63 %
    Favored  : 66.09 %
  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 aren not related in a simple way.
  whole:  0.83 (0.35), residues: 598
  helix:  1.52 (0.26), residues: 409
  sheet: -1.07 (1.14), residues: 18
  loop : -1.68 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 557 
 TYR   0.019   0.002   TYR A 724 
 PHE   0.024   0.002   PHE A 637 
 TRP   0.014   0.001   TRP B 546 
 HIS   0.006   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4834)
  covalent geometry    : angle       0.74986 ( 6607)
  SS BOND              : bond        0.00365 (    5)
  SS BOND              : angle       1.04679 (   10)
  hydrogen bonds       : bond        0.05211 (  292)
  hydrogen bonds       : angle       4.07994 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 90
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.8421 (tp30) cc_final: 0.7788 (tp30)
REVERT: A  555 GLN cc_start: 0.4661 (OUTLIER) cc_final: 0.4329 (pm20)
REVERT: A  654 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: A  672 TRP cc_start: 0.6936 (OUTLIER) cc_final: 0.6716 (t-100)
REVERT: A  689 LYS cc_start: 0.8953 (tppt) cc_final: 0.8588 (tptp)
REVERT: A  739 SER cc_start: 0.9297 (t) cc_final: 0.8966 (p)
REVERT: B  545 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7750 (mm-30)
REVERT: B  600 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: B  657 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: B  752 ARG cc_start: 0.7476 (ptm160) cc_final: 0.7036 (ptm160)
REVERT: B  768 MET cc_start: 0.9254 (mmp) cc_final: 0.8479 (mmp)
REVERT: B  816 LEU cc_start: 0.8830 (mt) cc_final: 0.8460 (tt)
  outliers start: 43
  outliers final: 30
  residues processed: 122
  average time/residue: 0.0572
  time to fit residues: 9.4609
Evaluate side-chains
  119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 86
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  555 GLN
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  600 GLN
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  637 GLN
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  647 CYS
Chi-restraints excluded: chain B residue  663 GLU
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  774 THR
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0870
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.130232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.108057 restraints weight = 11902.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.111168 restraints weight = 6475.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.113300 restraints weight = 4284.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.114645 restraints weight = 3224.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.115611 restraints weight = 2670.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.7438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4839  Z= 0.149
  Angle     :  0.763  12.165   6617  Z= 0.369
  Chirality :  0.041   0.151    778
  Planarity :  0.006   0.050    815
  Dihedral  :  4.374  18.161    650
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 28.71 %
    Favored  : 64.74 %
  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 aren not related in a simple way.
  whole:  0.71 (0.35), residues: 598
  helix:  1.44 (0.26), residues: 409
  sheet: -1.09 (1.10), residues: 16
  loop : -1.75 (0.45), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 557 
 TYR   0.018   0.002   TYR A 724 
 PHE   0.025   0.002   PHE A 637 
 TRP   0.010   0.001   TRP B 775 
 HIS   0.005   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4834)
  covalent geometry    : angle       0.76249 ( 6607)
  SS BOND              : bond        0.00426 (    5)
  SS BOND              : angle       0.98662 (   10)
  hydrogen bonds       : bond        0.04778 (  292)
  hydrogen bonds       : angle       4.05128 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 GLU cc_start: 0.8427 (tp30) cc_final: 0.7766 (tp30)
REVERT: A  555 GLN cc_start: 0.4678 (OUTLIER) cc_final: 0.4291 (pm20)
REVERT: A  654 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8268 (tm-30)
REVERT: A  689 LYS cc_start: 0.8942 (tppt) cc_final: 0.8588 (tptp)
REVERT: A  739 SER cc_start: 0.9311 (t) cc_final: 0.8978 (p)
REVERT: B  545 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8038 (mm-30)
REVERT: B  600 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7901 (pm20)
REVERT: B  657 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7826 (mm-30)
  outliers start: 34
  outliers final: 27
  residues processed: 113
  average time/residue: 0.0590
  time to fit residues: 9.0963
Evaluate side-chains
  114 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  555 GLN
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  600 GLN
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  637 GLN
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  774 THR
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    0.0070
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.131839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.109672 restraints weight = 11541.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.112882 restraints weight = 6288.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.114976 restraints weight = 4177.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.116357 restraints weight = 3153.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.117310 restraints weight = 2607.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.7664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4839  Z= 0.134
  Angle     :  0.748  11.279   6617  Z= 0.360
  Chirality :  0.040   0.141    778
  Planarity :  0.006   0.048    815
  Dihedral  :  4.263  16.773    650
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 29.87 %
    Favored  : 64.93 %
  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 aren not related in a simple way.
  whole:  0.89 (0.35), residues: 598
  helix:  1.59 (0.26), residues: 403
  sheet: -0.93 (1.10), residues: 16
  loop : -1.62 (0.44), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 557 
 TYR   0.018   0.001   TYR A 724 
 PHE   0.021   0.001   PHE B 703 
 TRP   0.008   0.001   TRP B 775 
 HIS   0.005   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4834)
  covalent geometry    : angle       0.74724 ( 6607)
  SS BOND              : bond        0.00377 (    5)
  SS BOND              : angle       1.03698 (   10)
  hydrogen bonds       : bond        0.04212 (  292)
  hydrogen bonds       : angle       3.89748 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  689 LYS cc_start: 0.8919 (tppt) cc_final: 0.8572 (tptp)
REVERT: A  739 SER cc_start: 0.9302 (t) cc_final: 0.8961 (p)
REVERT: B  545 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: B  657 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: B  734 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.6182 (t-90)
REVERT: B  768 MET cc_start: 0.9223 (mmp) cc_final: 0.8578 (mmp)
  outliers start: 27
  outliers final: 22
  residues processed: 111
  average time/residue: 0.0632
  time to fit residues: 9.4565
Evaluate side-chains
  111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  600 GLN
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  637 GLN
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0060
   chunk 21 optimal weight:    0.0010
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.3202

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.133167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.111180 restraints weight = 11663.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.114420 restraints weight = 6341.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.116543 restraints weight = 4183.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.117855 restraints weight = 3143.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.118910 restraints weight = 2608.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.7877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4839  Z= 0.131
  Angle     :  0.750  11.293   6617  Z= 0.360
  Chirality :  0.039   0.138    778
  Planarity :  0.006   0.047    815
  Dihedral  :  4.145  14.910    650
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 31.21 %
    Favored  : 64.93 %
  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 aren not related in a simple way.
  whole:  1.08 (0.35), residues: 598
  helix:  1.69 (0.26), residues: 404
  sheet: -0.72 (1.16), residues: 16
  loop : -1.46 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 557 
 TYR   0.025   0.001   TYR B 815 
 PHE   0.020   0.001   PHE B 703 
 TRP   0.007   0.001   TRP B 775 
 HIS   0.004   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4834)
  covalent geometry    : angle       0.74934 ( 6607)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       1.07386 (   10)
  hydrogen bonds       : bond        0.03832 (  292)
  hydrogen bonds       : angle       3.76746 (  870)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  546 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7627 (tt0)
REVERT: A  555 GLN cc_start: 0.4658 (OUTLIER) cc_final: 0.4289 (pm20)
REVERT: A  689 LYS cc_start: 0.8896 (tppt) cc_final: 0.8664 (tptt)
REVERT: A  739 SER cc_start: 0.9266 (t) cc_final: 0.8911 (p)
REVERT: B  545 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8087 (mm-30)
REVERT: B  657 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7650 (mm-30)
REVERT: B  717 GLU cc_start: 0.7204 (mp0) cc_final: 0.6943 (mp0)
REVERT: B  768 MET cc_start: 0.9212 (mmp) cc_final: 0.8548 (mmp)
  outliers start: 20
  outliers final: 19
  residues processed: 115
  average time/residue: 0.0561
  time to fit residues: 8.8932
Evaluate side-chains
  116 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  555 GLN
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  600 GLN
Chi-restraints excluded: chain B residue  613 CYS
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  637 GLN
Chi-restraints excluded: chain B residue  641 HIS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  759 ASN
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  787 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0050
   chunk 37 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.132945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.110736 restraints weight = 11660.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.113951 restraints weight = 6238.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.116110 restraints weight = 4096.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.117535 restraints weight = 3073.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.118423 restraints weight = 2523.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.7922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   4839  Z= 0.212
  Angle     :  1.230  59.167   6617  Z= 0.694
  Chirality :  0.042   0.373    778
  Planarity :  0.006   0.046    815
  Dihedral  :  4.168  14.801    650
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 31.79 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.18 %
  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 aren not related in a simple way.
  whole:  1.09 (0.35), residues: 598
  helix:  1.70 (0.26), residues: 404
  sheet: -0.69 (1.17), residues: 16
  loop : -1.46 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 557 
 TYR   0.017   0.001   TYR A 724 
 PHE   0.033   0.001   PHE A 637 
 TRP   0.007   0.001   TRP B 775 
 HIS   0.003   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 4834)
  covalent geometry    : angle       1.23035 ( 6607)
  SS BOND              : bond        0.00349 (    5)
  SS BOND              : angle       1.09729 (   10)
  hydrogen bonds       : bond        0.03848 (  292)
  hydrogen bonds       : angle       3.85412 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1049.82 seconds
wall clock time: 18 minutes 48.11 seconds (1128.11 seconds total)