Starting phenix.real_space_refine
on Fri Aug 22 14:18:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2025/9iiz_60610.cif"
  }
  resolution = 3.8
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      49      5.49       5
     S      20      5.16       5
     C    2414      2.51       5
     N     708      2.21       5
     O     889      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4080
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3043
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 356}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 529
          Classifications: {'RNA': 25}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 12, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 22}
    Chain: "C"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 508
          Classifications: {'RNA': 24}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12}
          Link IDs: {'rna3p': 23}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.34, per 1000 atoms: 0.33
  Number of scatterers: 4080
  At special positions: 0
  Unit cell: (66.4884, 83.6142, 100.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      49     15.00
     O     889      8.00
     N     708      7.00
     C    2414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 127.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  724

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      35.8% alpha, 13.3% beta
      20 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 605 through 611
    Processing helix  chain 'A' and resid 628 through 630
      No H-bonds generated for 'chain 'A' and resid 628 through 630'
    Processing helix  chain 'A' and resid 631 through 640
    Processing helix  chain 'A' and resid 641 through 644
    Processing helix  chain 'A' and resid 645 through 650
      removed outlier: 3.520A  pdb=" N   ILE A 649 " --> pdb=" O   VAL A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 675
    Processing helix  chain 'A' and resid 692 through 704
      removed outlier: 3.531A  pdb=" N   TYR A 696 " --> pdb=" O   ARG A 692 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS A 704 " --> pdb=" O   LYS A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 739
      removed outlier: 4.041A  pdb=" N   VAL A 728 " --> pdb=" O   LYS A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 819
      removed outlier: 4.332A  pdb=" N   HIS A 801 " --> pdb=" O   GLN A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 836 through 848
      removed outlier: 4.299A  pdb=" N   VAL A 845 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
      Proline residue:  A 846  - end of helix
    Processing helix  chain 'A' and resid 930 through 941
    Processing helix  chain 'A' and resid 955 through 971
      removed outlier: 3.780A  pdb=" N   ASN A 959 " --> pdb=" O   PRO A 955 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   SER A 971 " --> pdb=" O   LEU A 967 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 592
    Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 660
      removed outlier: 6.411A  pdb=" N   ALA A 624 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   VAL A 687 " --> pdb=" O   ALA A 624 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU A 626 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   VAL A 684 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU A 714 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   ILE A 686 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 791
      removed outlier: 4.120A  pdb=" N   ALA A 791 " --> pdb=" O   ALA A 773 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ALA A 773 " --> pdb=" O   ALA A 791 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   VAL A 756 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE A 826 " --> pdb=" O   MET A 755 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   ILE A 825 " --> pdb=" O   ALA A 864 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   VAL A 866 " --> pdb=" O   ILE A 825 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 827 " --> pdb=" O   VAL A 866 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   VAL A 868 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   VAL A 865 " --> pdb=" O   ILE A 923 " (cutoff:3.500A)

    104 hydrogen bonds defined for protein.
    300 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      96 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1114
        1.34 -     1.46: 1247
        1.46 -     1.58: 1783
        1.58 -     1.71: 96
        1.71 -     1.83: 31
  Bond restraints: 4271
  Sorted by residual:
  bond pdb=" P     G B  22 "
       pdb=" O5'   G B  22 "
    ideal  model  delta    sigma   weight residual
    1.593  1.625 -0.032 1.50e-02 4.44e+03 4.54e+00
  bond pdb=" O5'   G B  22 "
       pdb=" C5'   G B  22 "
    ideal  model  delta    sigma   weight residual
    1.420  1.451 -0.031 1.50e-02 4.44e+03 4.36e+00
  bond pdb=" CB  ASP A 982 "
       pdb=" CG  ASP A 982 "
    ideal  model  delta    sigma   weight residual
    1.516  1.563 -0.047 2.50e-02 1.60e+03 3.61e+00
  bond pdb=" P     G B  23 "
       pdb=" OP2   G B  23 "
    ideal  model  delta    sigma   weight residual
    1.485  1.522 -0.037 2.00e-02 2.50e+03 3.38e+00
  bond pdb=" CA  LYS A 739 "
       pdb=" C   LYS A 739 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.025 1.38e-02 5.25e+03 3.21e+00
  ... (remaining 4266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.72: 5904
        3.72 -     7.44: 84
        7.44 -    11.17: 16
       11.17 -    14.89: 4
       14.89 -    18.61: 3
  Bond angle restraints: 6011
  Sorted by residual:
  angle pdb=" CA  LYS A 739 "
        pdb=" CB  LYS A 739 "
        pdb=" CG  LYS A 739 "
      ideal   model   delta    sigma   weight residual
     114.10  127.96  -13.86 2.00e+00 2.50e-01 4.81e+01
  angle pdb=" CB  MET A 736 "
        pdb=" CG  MET A 736 "
        pdb=" SD  MET A 736 "
      ideal   model   delta    sigma   weight residual
     112.70  131.31  -18.61 3.00e+00 1.11e-01 3.85e+01
  angle pdb=" CA  MET A 736 "
        pdb=" CB  MET A 736 "
        pdb=" CG  MET A 736 "
      ideal   model   delta    sigma   weight residual
     114.10  125.95  -11.85 2.00e+00 2.50e-01 3.51e+01
  angle pdb=" C   LEU A 984 "
        pdb=" N   PHE A 985 "
        pdb=" CA  PHE A 985 "
      ideal   model   delta    sigma   weight residual
     120.38  128.07   -7.69 1.46e+00 4.69e-01 2.78e+01
  angle pdb=" CA  LEU A 967 "
        pdb=" CB  LEU A 967 "
        pdb=" CG  LEU A 967 "
      ideal   model   delta    sigma   weight residual
     116.30  134.49  -18.19 3.50e+00 8.16e-02 2.70e+01
  ... (remaining 6006 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.79: 2386
       32.79 -    65.58: 225
       65.58 -    98.37: 27
       98.37 -   131.16: 2
      131.16 -   163.95: 1
  Dihedral angle restraints: 2641
    sinusoidal: 1525
      harmonic: 1116
  Sorted by residual:
  dihedral pdb=" CA  HIS A 943 "
           pdb=" C   HIS A 943 "
           pdb=" N   MET A 944 "
           pdb=" CA  MET A 944 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.98   23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" O4'   U B  25 "
           pdb=" C1'   U B  25 "
           pdb=" N1    U B  25 "
           pdb=" C2    U B  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -62.62  -65.38     1      1.70e+01 3.46e-03 1.94e+01
  dihedral pdb=" O4'   U B   1 "
           pdb=" C1'   U B   1 "
           pdb=" N1    U B   1 "
           pdb=" C2    U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -70.13  -57.87     1      1.70e+01 3.46e-03 1.56e+01
  ... (remaining 2638 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 659
       0.112 -    0.223: 46
       0.223 -    0.335: 2
       0.335 -    0.446: 1
       0.446 -    0.558: 3
  Chirality restraints: 711
  Sorted by residual:
  chirality pdb=" P     G B  22 "
            pdb=" OP1   G B  22 "
            pdb=" OP2   G B  22 "
            pdb=" O5'   G B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.78e+00
  chirality pdb=" P     G B  23 "
            pdb=" OP1   G B  23 "
            pdb=" OP2   G B  23 "
            pdb=" O5'   G B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" P     U B  25 "
            pdb=" OP1   U B  25 "
            pdb=" OP2   U B  25 "
            pdb=" O5'   U B  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.89   -0.48 2.00e-01 2.50e+01 5.85e+00
  ... (remaining 708 not shown)

  Planarity restraints: 585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 646 "   -0.043 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO A 647 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 647 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 647 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 647 "   -0.042 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO A 648 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 648 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 648 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 678 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.28e+00
        pdb=" N   PRO A 679 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 679 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 679 "    0.032 5.00e-02 4.00e+02
  ... (remaining 582 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 913
        2.79 -     3.31: 3616
        3.31 -     3.84: 8013
        3.84 -     4.37: 8518
        4.37 -     4.90: 12876
  Nonbonded interactions: 33936
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 934 "
            pdb=" OG1 THR A 938 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NE2 GLN A 793 "
            pdb=" O   GLN A 795 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" NE2 GLN A 712 "
            pdb=" OE1 GLN A 735 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OG1 THR A 954 "
            pdb=" OD1 ASN A 959 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASP A 760 "
            pdb=" OD2 ASP A 830 "
     model   vdw
     2.324 3.040
  ... (remaining 33931 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.070
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6054
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      :  0.005   0.054   4271  Z= 0.261
  Angle     :  1.234  18.610   6011  Z= 0.595
  Chirality :  0.068   0.558    711
  Planarity :  0.007   0.064    585
  Dihedral  : 22.766 163.954   1917
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 29.79 %
    Favored  : 69.62 %
  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: -3.44 (0.38), residues: 373
  helix: -2.03 (0.41), residues: 118
  sheet: -0.75 (0.64), residues: 72
  loop : -3.17 (0.38), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 726 
 TYR   0.024   0.002   TYR A 901 
 PHE   0.037   0.002   PHE A 986 
 TRP   0.022   0.003   TRP A 745 
 HIS   0.004   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 4271)
  covalent geometry    : angle       1.23412 ( 6011)
  hydrogen bonds       : bond        0.15622 (  152)
  hydrogen bonds       : angle       7.60011 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  755 MET cc_start: -0.2981 (ptt) cc_final: -0.3284 (ptt)
  outliers start: 2
  outliers final: 2
  residues processed: 68
  average time/residue: 0.0899
  time to fit residues: 7.3930
Evaluate side-chains
  63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0000
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0070
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.7804

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

Flipped N/Q/H residues before XYZ refinement:
A 962 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.183166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.162004 restraints weight = 11891.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.166750 restraints weight = 7483.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.170085 restraints weight = 5143.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.172475 restraints weight = 3779.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.174276 restraints weight = 2917.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6115
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4271  Z= 0.136
  Angle     :  0.760  11.603   6011  Z= 0.362
  Chirality :  0.044   0.246    711
  Planarity :  0.005   0.051    585
  Dihedral  : 22.678 153.879   1160
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 29.50 %
    Favored  : 68.44 %
  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: -2.69 (0.41), residues: 373
  helix: -0.95 (0.45), residues: 116
  sheet: -0.94 (0.62), residues: 78
  loop : -2.80 (0.41), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 726 
 TYR   0.006   0.001   TYR A 787 
 PHE   0.009   0.001   PHE A 985 
 TRP   0.009   0.001   TRP A 786 
 HIS   0.005   0.001   HIS A 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4271)
  covalent geometry    : angle       0.75980 ( 6011)
  hydrogen bonds       : bond        0.05543 (  152)
  hydrogen bonds       : angle       5.32192 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  736 MET cc_start: 0.8141 (mpp) cc_final: 0.7764 (mpp)
REVERT: A  748 GLU cc_start: 0.8139 (pp20) cc_final: 0.7894 (pp20)
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0913
  time to fit residues: 7.3954
Evaluate side-chains
  63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  962 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:   30.0000
   chunk 31 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 962 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.175641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.154205 restraints weight = 12054.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.158916 restraints weight = 7569.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.162230 restraints weight = 5273.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.164756 restraints weight = 3906.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.166551 restraints weight = 3018.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6300
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4271  Z= 0.189
  Angle     :  0.819  12.354   6011  Z= 0.387
  Chirality :  0.044   0.201    711
  Planarity :  0.005   0.047    585
  Dihedral  : 22.756 158.498   1159
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 20.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.43 %
    Favored  : 67.85 %
  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: -2.39 (0.42), residues: 373
  helix: -0.48 (0.46), residues: 116
  sheet: -1.16 (0.61), residues: 78
  loop : -2.58 (0.44), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 671 
 TYR   0.012   0.002   TYR A 669 
 PHE   0.010   0.001   PHE A 985 
 TRP   0.010   0.002   TRP A 745 
 HIS   0.014   0.001   HIS A 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4271)
  covalent geometry    : angle       0.81863 ( 6011)
  hydrogen bonds       : bond        0.06471 (  152)
  hydrogen bonds       : angle       5.40756 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  674 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6170 (ttm170)
  outliers start: 16
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0787
  time to fit residues: 6.9498
Evaluate side-chains
  66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  674 ARG
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  987 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0170
   chunk 16 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
A 763 HIS
A 818 ASN
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.169070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.146272 restraints weight = 11955.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.151061 restraints weight = 7605.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.154374 restraints weight = 5350.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.156597 restraints weight = 4023.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.158493 restraints weight = 3210.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4271  Z= 0.255
  Angle     :  0.887  12.046   6011  Z= 0.429
  Chirality :  0.046   0.218    711
  Planarity :  0.006   0.048    585
  Dihedral  : 23.058 161.066   1159
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 26.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 32.15 %
    Favored  : 62.83 %
  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: -2.47 (0.42), residues: 373
  helix: -0.40 (0.46), residues: 110
  sheet: -1.49 (0.61), residues: 78
  loop : -2.52 (0.44), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 671 
 TYR   0.014   0.002   TYR A 945 
 PHE   0.015   0.002   PHE A 985 
 TRP   0.011   0.002   TRP A 623 
 HIS   0.005   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 4271)
  covalent geometry    : angle       0.88749 ( 6011)
  hydrogen bonds       : bond        0.08142 (  152)
  hydrogen bonds       : angle       6.06316 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0759
  time to fit residues: 6.9177
Evaluate side-chains
  66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  606 SER
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  849 ASN
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  943 HIS
Chi-restraints excluded: chain A residue  987 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.0670
   chunk 31 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
A 763 HIS
A 818 ASN
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.177051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.155023 restraints weight = 12132.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.159792 restraints weight = 7896.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.163149 restraints weight = 5532.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.165482 restraints weight = 4129.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.167317 restraints weight = 3244.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6275
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4271  Z= 0.145
  Angle     :  0.771  12.489   6011  Z= 0.367
  Chirality :  0.044   0.192    711
  Planarity :  0.005   0.049    585
  Dihedral  : 22.428 153.658   1158
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 32.15 %
    Favored  : 62.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.43), residues: 373
  helix:  0.05 (0.49), residues: 109
  sheet: -1.19 (0.62), residues: 80
  loop : -2.44 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 671 
 TYR   0.011   0.001   TYR A 669 
 PHE   0.012   0.001   PHE A 985 
 TRP   0.013   0.001   TRP A 745 
 HIS   0.003   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4271)
  covalent geometry    : angle       0.77071 ( 6011)
  hydrogen bonds       : bond        0.05671 (  152)
  hydrogen bonds       : angle       5.24513 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  683 MET cc_start: 0.0633 (ttt) cc_final: 0.0324 (ptm)
  outliers start: 18
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0668
  time to fit residues: 6.1265
Evaluate side-chains
  69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  606 SER
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  818 ASN
Chi-restraints excluded: chain A residue  849 ASN
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  915 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 818 ASN
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 962 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.172564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.150183 restraints weight = 12487.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.155036 restraints weight = 8100.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.158452 restraints weight = 5698.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.160830 restraints weight = 4237.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.162626 restraints weight = 3322.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4271  Z= 0.189
  Angle     :  0.812  12.396   6011  Z= 0.392
  Chirality :  0.045   0.203    711
  Planarity :  0.005   0.050    585
  Dihedral  : 22.604 156.818   1158
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 23.83
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 10.46 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 33.33 %
    Favored  : 61.06 %
  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: -2.21 (0.43), residues: 373
  helix: -0.02 (0.49), residues: 108
  sheet: -1.16 (0.64), residues: 78
  loop : -2.54 (0.43), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 671 
 TYR   0.026   0.002   TYR A 669 
 PHE   0.013   0.002   PHE A 638 
 TRP   0.014   0.002   TRP A 745 
 HIS   0.007   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4271)
  covalent geometry    : angle       0.81175 ( 6011)
  hydrogen bonds       : bond        0.06592 (  152)
  hydrogen bonds       : angle       5.53542 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  844 GLU cc_start: 0.2806 (OUTLIER) cc_final: 0.2178 (mp0)
  outliers start: 19
  outliers final: 15
  residues processed: 71
  average time/residue: 0.0677
  time to fit residues: 5.9940
Evaluate side-chains
  72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  606 SER
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  818 ASN
Chi-restraints excluded: chain A residue  844 GLU
Chi-restraints excluded: chain A residue  849 ASN
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  962 HIS
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0470
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 962 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.175634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.152646 restraints weight = 12378.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.157500 restraints weight = 8006.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.160918 restraints weight = 5668.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.163580 restraints weight = 4272.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.165469 restraints weight = 3331.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6321
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4271  Z= 0.155
  Angle     :  0.792  12.580   6011  Z= 0.377
  Chirality :  0.044   0.195    711
  Planarity :  0.005   0.061    585
  Dihedral  : 22.422 154.748   1158
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 35.10 %
    Favored  : 59.88 %
  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: -2.07 (0.44), residues: 373
  helix:  0.10 (0.49), residues: 109
  sheet: -1.03 (0.64), residues: 78
  loop : -2.51 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 671 
 TYR   0.023   0.002   TYR A 669 
 PHE   0.012   0.002   PHE A 985 
 TRP   0.027   0.002   TRP A 745 
 HIS   0.016   0.002   HIS A 962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4271)
  covalent geometry    : angle       0.79159 ( 6011)
  hydrogen bonds       : bond        0.05745 (  152)
  hydrogen bonds       : angle       5.33348 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  723 GLN cc_start: 0.8258 (pp30) cc_final: 0.7970 (pp30)
REVERT: A  844 GLU cc_start: 0.2861 (OUTLIER) cc_final: 0.2402 (mp0)
  outliers start: 17
  outliers final: 14
  residues processed: 70
  average time/residue: 0.0771
  time to fit residues: 6.6614
Evaluate side-chains
  73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  844 GLU
Chi-restraints excluded: chain A residue  849 ASN
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0970
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 682 GLN
** A 943 HIS ** 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 = 0.4519 r_free = 0.4519 target = 0.179452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.158279 restraints weight = 12158.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.162940 restraints weight = 7739.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.166316 restraints weight = 5377.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.168925 restraints weight = 3951.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.170799 restraints weight = 3007.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6212
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4271  Z= 0.135
  Angle     :  0.761  13.229   6011  Z= 0.361
  Chirality :  0.043   0.194    711
  Planarity :  0.004   0.050    585
  Dihedral  : 22.106 151.967   1158
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 35.40 %
    Favored  : 59.29 %
  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: -2.06 (0.44), residues: 373
  helix:  0.11 (0.49), residues: 115
  sheet: -1.04 (0.64), residues: 78
  loop : -2.57 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 671 
 TYR   0.035   0.002   TYR A 669 
 PHE   0.013   0.002   PHE A 852 
 TRP   0.026   0.002   TRP A 745 
 HIS   0.003   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4271)
  covalent geometry    : angle       0.76131 ( 6011)
  hydrogen bonds       : bond        0.05154 (  152)
  hydrogen bonds       : angle       5.06864 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.4046 (ppp) cc_final: 0.3327 (ppp)
REVERT: A  683 MET cc_start: 0.0759 (ptm) cc_final: -0.0068 (ptm)
REVERT: A  723 GLN cc_start: 0.8208 (pp30) cc_final: 0.7970 (pp30)
REVERT: A  844 GLU cc_start: 0.2960 (OUTLIER) cc_final: 0.2357 (mp0)
REVERT: A  921 ARG cc_start: 0.8325 (tpm170) cc_final: 0.8055 (ptp-170)
  outliers start: 18
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0580
  time to fit residues: 5.9681
Evaluate side-chains
  76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  682 GLN
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  844 GLU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  987 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 682 GLN
** A 943 HIS ** 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 = 0.4496 r_free = 0.4496 target = 0.177354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.156148 restraints weight = 12534.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.160894 restraints weight = 7898.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.164303 restraints weight = 5458.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.166794 restraints weight = 4008.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.168587 restraints weight = 3083.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4271  Z= 0.148
  Angle     :  0.810  15.261   6011  Z= 0.376
  Chirality :  0.044   0.201    711
  Planarity :  0.005   0.049    585
  Dihedral  : 22.193 152.679   1158
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 21.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 35.69 %
    Favored  : 59.29 %
  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: -2.04 (0.44), residues: 373
  helix:  0.14 (0.49), residues: 116
  sheet: -0.96 (0.64), residues: 77
  loop : -2.62 (0.44), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 671 
 TYR   0.050   0.002   TYR A 669 
 PHE   0.013   0.002   PHE A 852 
 TRP   0.027   0.002   TRP A 745 
 HIS   0.004   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4271)
  covalent geometry    : angle       0.80962 ( 6011)
  hydrogen bonds       : bond        0.05368 (  152)
  hydrogen bonds       : angle       5.17913 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  589 LYS cc_start: 0.8913 (tppp) cc_final: 0.8489 (tppt)
REVERT: A  601 MET cc_start: 0.3949 (ppp) cc_final: 0.3222 (ppp)
REVERT: A  683 MET cc_start: 0.1441 (ptm) cc_final: 0.0636 (ptm)
REVERT: A  723 GLN cc_start: 0.8207 (pp30) cc_final: 0.7943 (pp30)
REVERT: A  844 GLU cc_start: 0.3058 (OUTLIER) cc_final: 0.2418 (mp0)
  outliers start: 17
  outliers final: 15
  residues processed: 77
  average time/residue: 0.0673
  time to fit residues: 6.5093
Evaluate side-chains
  74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  844 GLU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  987 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0030
   chunk 18 optimal weight:   50.0000
   chunk 36 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0980
   chunk 26 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.0594

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

Flipped N/Q/H residues before XYZ refinement:
** A 943 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 = 0.4506 r_free = 0.4506 target = 0.178367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.156507 restraints weight = 12263.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.161364 restraints weight = 7642.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.164822 restraints weight = 5284.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.167395 restraints weight = 3893.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.169257 restraints weight = 2993.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6255
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4271  Z= 0.144
  Angle     :  0.810  15.293   6011  Z= 0.378
  Chirality :  0.044   0.197    711
  Planarity :  0.005   0.048    585
  Dihedral  : 22.149 152.632   1158
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 36.87 %
    Favored  : 58.70 %
  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: -2.12 (0.44), residues: 373
  helix: -0.10 (0.48), residues: 122
  sheet: -1.24 (0.68), residues: 65
  loop : -2.42 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 671 
 TYR   0.042   0.002   TYR A 669 
 PHE   0.011   0.001   PHE A 852 
 TRP   0.027   0.002   TRP A 745 
 HIS   0.003   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4271)
  covalent geometry    : angle       0.80980 ( 6011)
  hydrogen bonds       : bond        0.05201 (  152)
  hydrogen bonds       : angle       5.11261 (  396)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.3920 (ppp) cc_final: 0.3192 (ppp)
REVERT: A  676 LEU cc_start: -0.2037 (OUTLIER) cc_final: -0.2814 (mt)
REVERT: A  683 MET cc_start: 0.1216 (ptm) cc_final: 0.0379 (ptm)
REVERT: A  723 GLN cc_start: 0.8191 (pp30) cc_final: 0.7926 (pp30)
REVERT: A  844 GLU cc_start: 0.3047 (OUTLIER) cc_final: 0.2425 (mp0)
  outliers start: 15
  outliers final: 12
  residues processed: 75
  average time/residue: 0.0653
  time to fit residues: 6.2990
Evaluate side-chains
  72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  844 GLU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  987 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 ASN
** A 943 HIS ** 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 = 0.4415 r_free = 0.4415 target = 0.171392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.149475 restraints weight = 12570.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.154217 restraints weight = 7975.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.157486 restraints weight = 5563.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.159897 restraints weight = 4160.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.161679 restraints weight = 3250.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4271  Z= 0.214
  Angle     :  0.881  15.124   6011  Z= 0.420
  Chirality :  0.047   0.236    711
  Planarity :  0.005   0.047    585
  Dihedral  : 22.617 157.013   1158
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 26.70
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.58 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 35.69 %
    Favored  : 58.41 %
  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: -2.37 (0.43), residues: 373
  helix: -0.25 (0.47), residues: 116
  sheet: -1.28 (0.65), residues: 77
  loop : -2.66 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 671 
 TYR   0.041   0.002   TYR A 669 
 PHE   0.011   0.002   PHE A 985 
 TRP   0.024   0.003   TRP A 745 
 HIS   0.006   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 4271)
  covalent geometry    : angle       0.88084 ( 6011)
  hydrogen bonds       : bond        0.06625 (  152)
  hydrogen bonds       : angle       5.61963 (  396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 881.57 seconds
wall clock time: 15 minutes 55.47 seconds (955.47 seconds total)