Starting phenix.real_space_refine
on Fri Aug 22 12:58:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b2u_44115/08_2025/9b2u_44115_neut.cif"
  }
  resolution = 3.64
  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=   0.010
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      15      5.16       5
     C    1705      2.51       5
     N     456      2.21       5
     O     496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 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: 2672
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "E"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 36
          Classifications: {'peptide': 4}
          Link IDs: {'TRANS': 3}
    Chain: "K"
      Number of atoms: 2636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2636
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 316}
  Time building chain proxies: 0.97, per 1000 atoms: 0.36
  Number of scatterers: 2672
  At special positions: 0
  Unit cell: (67.9, 74.69, 61.11, 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      15     16.00
     O     496      8.00
     N     456      7.00
     C    1705      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: 0.22
  Conformation dependent library (CDL) restraints added in 113.5 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  626

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 5 sheets defined
      42.0% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'K' and resid 474 through 479
      removed outlier: 4.039A  pdb=" N   CYS K 478 " --> pdb=" O   PRO K 474 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 480 through 486
      removed outlier: 3.537A  pdb=" N   ARG K 486 " --> pdb=" O   GLU K 482 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 528 through 545
      Proline residue:  K 534  - end of helix
      removed outlier: 3.537A  pdb=" N   LEU K 545 " --> pdb=" O   GLU K 541 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 546 through 548
      No H-bonds generated for 'chain 'K' and resid 546 through 548'
    Processing helix  chain 'K' and resid 570 through 584
      removed outlier: 3.534A  pdb=" N   LEU K 574 " --> pdb=" O   PRO K 570 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 613 through 615
      No H-bonds generated for 'chain 'K' and resid 613 through 615'
    Processing helix  chain 'K' and resid 621 through 644
    Processing helix  chain 'K' and resid 708 through 713
      removed outlier: 3.541A  pdb=" N   THR K 712 " --> pdb=" O   ASP K 709 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLY K 713 " --> pdb=" O   LEU K 710 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 716 through 729
      removed outlier: 4.020A  pdb=" N   TYR K 722 " --> pdb=" O   GLN K 718 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ARG K 723 " --> pdb=" O   PHE K 719 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 738 through 755
      removed outlier: 4.049A  pdb=" N   VAL K 742 " --> pdb=" O   PRO K 738 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU K 743 " --> pdb=" O   TYR K 739 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TRP K 744 " --> pdb=" O   SER K 740 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 764 through 780
    Processing helix  chain 'K' and resid 786 through 794
    Processing sheet with id=AA1, first strand: chain 'K' and resid 472 through 473
      removed outlier: 6.047A  pdb=" N   VAL K 473 " --> pdb=" O   GLN K 566 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LEU K 559 " --> pdb=" O   GLU K 606 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   GLU K 606 " --> pdb=" O   LEU K 559 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   SER K 561 " --> pdb=" O   GLU K 604 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   HIS K 563 " --> pdb=" O   VAL K 602 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU K 599 " --> pdb=" O   ILE K 515 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE K 515 " --> pdb=" O   LEU K 599 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLY K 496 " --> pdb=" O   GLU K 492 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   GLU K 492 " --> pdb=" O   GLY K 496 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   VAL K 498 " --> pdb=" O   ILE K 490 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 520 through 521
    Processing sheet with id=AA3, first strand: chain 'K' and resid 610 through 611
      removed outlier: 3.501A  pdb=" N   ILE K 610 " --> pdb=" O   LEU K 657 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 664 through 669
    Processing sheet with id=AA5, first strand: chain 'K' and resid 693 through 695

    117 hydrogen bonds defined for protein.
    333 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: 0.26

  Time building geometry restraints manager: 0.31 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: 864
        1.34 -     1.46: 602
        1.46 -     1.58: 1242
        1.58 -     1.70: 0
        1.70 -     1.81: 22
  Bond restraints: 2730
  Sorted by residual:
  bond pdb=" N   LYS E   4 "
       pdb=" CA  LYS E   4 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.21e-02 6.83e+03 6.71e+00
  bond pdb=" N   THR E   3 "
       pdb=" CA  THR E   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.84e+00
  bond pdb=" N   ARG E   2 "
       pdb=" CA  ARG E   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.59e+00
  bond pdb=" N   GLN E   5 "
       pdb=" CA  GLN E   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.48e+00
  bond pdb=" CB  ASP K 696 "
       pdb=" CG  ASP K 696 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 2.50e-02 1.60e+03 1.99e+00
  ... (remaining 2725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 3538
        1.71 -     3.41: 121
        3.41 -     5.12: 14
        5.12 -     6.83: 6
        6.83 -     8.54: 4
  Bond angle restraints: 3683
  Sorted by residual:
  angle pdb=" CA  LYS K 489 "
        pdb=" CB  LYS K 489 "
        pdb=" CG  LYS K 489 "
      ideal   model   delta    sigma   weight residual
     114.10  120.96   -6.86 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" CA  GLU K 606 "
        pdb=" CB  GLU K 606 "
        pdb=" CG  GLU K 606 "
      ideal   model   delta    sigma   weight residual
     114.10  120.07   -5.97 2.00e+00 2.50e-01 8.90e+00
  angle pdb=" C   THR K 528 "
        pdb=" CA  THR K 528 "
        pdb=" CB  THR K 528 "
      ideal   model   delta    sigma   weight residual
     109.66  115.16   -5.50 1.94e+00 2.66e-01 8.03e+00
  angle pdb=" CA  LEU K 484 "
        pdb=" CB  LEU K 484 "
        pdb=" CG  LEU K 484 "
      ideal   model   delta    sigma   weight residual
     116.30  124.84   -8.54 3.50e+00 8.16e-02 5.95e+00
  angle pdb=" N   PHE K 529 "
        pdb=" CA  PHE K 529 "
        pdb=" C   PHE K 529 "
      ideal   model   delta    sigma   weight residual
     111.28  113.87   -2.59 1.09e+00 8.42e-01 5.64e+00
  ... (remaining 3678 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 1375
       17.84 -    35.68: 211
       35.68 -    53.52: 46
       53.52 -    71.36: 5
       71.36 -    89.20: 7
  Dihedral angle restraints: 1644
    sinusoidal: 678
      harmonic: 966
  Sorted by residual:
  dihedral pdb=" CA  HIS K 647 "
           pdb=" C   HIS K 647 "
           pdb=" N   ARG K 648 "
           pdb=" CA  ARG K 648 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.74   22.26     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  PHE K 593 "
           pdb=" C   PHE K 593 "
           pdb=" N   PHE K 594 "
           pdb=" CA  PHE K 594 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.46  -16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  LEU K 650 "
           pdb=" C   LEU K 650 "
           pdb=" N   HIS K 651 "
           pdb=" CA  HIS K 651 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.52   16.48     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 1641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 211
       0.027 -    0.053: 106
       0.053 -    0.080: 56
       0.080 -    0.107: 28
       0.107 -    0.133: 9
  Chirality restraints: 410
  Sorted by residual:
  chirality pdb=" CA  ILE K 515 "
            pdb=" N   ILE K 515 "
            pdb=" C   ILE K 515 "
            pdb=" CB  ILE K 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  ILE K 513 "
            pdb=" N   ILE K 513 "
            pdb=" C   ILE K 513 "
            pdb=" CB  ILE K 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ASN K 730 "
            pdb=" N   ASN K 730 "
            pdb=" C   ASN K 730 "
            pdb=" CB  ASN K 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 407 not shown)

  Planarity restraints: 468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP K 696 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.69e+00
        pdb=" C   ASP K 696 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASP K 696 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY K 697 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 577 "   -0.016 2.00e-02 2.50e+03   1.18e-02 3.48e+00
        pdb=" CG  TRP K 577 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 577 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 577 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 577 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 577 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 577 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 577 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 577 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 577 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K 722 "    0.014 2.00e-02 2.50e+03   1.15e-02 2.64e+00
        pdb=" CG  TYR K 722 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR K 722 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR K 722 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR K 722 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR K 722 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR K 722 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR K 722 "    0.000 2.00e-02 2.50e+03
  ... (remaining 465 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 75
        2.70 -     3.25: 2729
        3.25 -     3.80: 4074
        3.80 -     4.35: 5227
        4.35 -     4.90: 8389
  Nonbonded interactions: 20494
  Sorted by model distance:
  nonbonded pdb=" OG  SER K 546 "
            pdb=" O   THR K 553 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   SER K 621 "
            pdb=" OG1 THR K 624 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OE2 GLU K 640 "
            pdb=" ND2 ASN K 741 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   VAL K 562 "
            pdb=" ND1 HIS K 563 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" N   ASP K 709 "
            pdb=" OD1 ASP K 709 "
     model   vdw
     2.342 3.120
  ... (remaining 20489 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:             6.980
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.080
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5589
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2730  Z= 0.176
  Angle     :  0.777   8.536   3683  Z= 0.420
  Chirality :  0.045   0.133    410
  Planarity :  0.003   0.022    468
  Dihedral  : 17.956  89.198   1018
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 30.67 %
    Favored  : 68.67 %
  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: -0.49 (0.45), residues: 329
  helix:  0.43 (0.49), residues: 111
  sheet:  1.27 (0.73), residues: 52
  loop : -1.42 (0.46), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 590 
 TYR   0.028   0.002   TYR K 722 
 PHE   0.018   0.002   PHE K 594 
 TRP   0.032   0.003   TRP K 577 
 HIS   0.003   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2730)
  covalent geometry    : angle       0.77706 ( 3683)
  hydrogen bonds       : bond        0.19402 (  117)
  hydrogen bonds       : angle       7.48204 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: K  552 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6328 (ttp80)
REVERT: K  572 LEU cc_start: 0.6421 (mp) cc_final: 0.6128 (mp)
REVERT: K  644 ARG cc_start: 0.6542 (ttm170) cc_final: 0.5533 (ttm110)
REVERT: K  738 PRO cc_start: 0.7661 (Cg_endo) cc_final: 0.7409 (Cg_exo)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.0804
  time to fit residues: 5.3623
Evaluate side-chains
  41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  709 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0010
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
E   5 GLN
K 500 GLN
K 737 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.223458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.196028 restraints weight = 3552.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.197267 restraints weight = 2383.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.199288 restraints weight = 1893.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.200107 restraints weight = 1486.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.200957 restraints weight = 1178.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2730  Z= 0.134
  Angle     :  0.657   8.581   3683  Z= 0.329
  Chirality :  0.046   0.163    410
  Planarity :  0.004   0.027    468
  Dihedral  :  4.882  18.381    356
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 24.33 %
    Favored  : 67.67 %
  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: -0.37 (0.47), residues: 329
  helix:  0.55 (0.50), residues: 117
  sheet:  1.34 (0.69), residues: 60
  loop : -1.58 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 723 
 TYR   0.016   0.002   TYR K 722 
 PHE   0.009   0.001   PHE K 600 
 TRP   0.017   0.002   TRP K 577 
 HIS   0.003   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2730)
  covalent geometry    : angle       0.65707 ( 3683)
  hydrogen bonds       : bond        0.04496 (  117)
  hydrogen bonds       : angle       5.37620 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5848 (mt)
REVERT: K  688 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.5282 (m-80)
REVERT: K  700 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6768 (t)
REVERT: K  706 MET cc_start: 0.3961 (OUTLIER) cc_final: 0.2141 (ptp)
  outliers start: 24
  outliers final: 5
  residues processed: 65
  average time/residue: 0.0762
  time to fit residues: 5.8245
Evaluate side-chains
  46 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  528 THR
Chi-restraints excluded: chain K residue  572 LEU
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  688 TYR
Chi-restraints excluded: chain K residue  700 VAL
Chi-restraints excluded: chain K residue  706 MET
Chi-restraints excluded: chain K residue  750 ASP
Chi-restraints excluded: chain K residue  760 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0670
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.216178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.188199 restraints weight = 3645.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.188437 restraints weight = 2932.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.191659 restraints weight = 2124.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.192325 restraints weight = 1553.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.192836 restraints weight = 1279.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2730  Z= 0.172
  Angle     :  0.678  10.246   3683  Z= 0.344
  Chirality :  0.046   0.134    410
  Planarity :  0.004   0.039    468
  Dihedral  :  5.050  15.959    354
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 21.33 %
    Favored  : 71.67 %
  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: -0.74 (0.45), residues: 329
  helix:  0.16 (0.48), residues: 117
  sheet:  1.10 (0.68), residues: 60
  loop : -1.71 (0.46), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 648 
 TYR   0.018   0.002   TYR K 580 
 PHE   0.019   0.002   PHE K 594 
 TRP   0.021   0.003   TRP K 577 
 HIS   0.004   0.001   HIS K 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 2730)
  covalent geometry    : angle       0.67797 ( 3683)
  hydrogen bonds       : bond        0.04739 (  117)
  hydrogen bonds       : angle       5.26685 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5852 (mt)
REVERT: K  672 LYS cc_start: 0.5680 (tppt) cc_final: 0.4589 (ptpt)
REVERT: K  706 MET cc_start: 0.4477 (OUTLIER) cc_final: 0.2506 (ptp)
  outliers start: 21
  outliers final: 10
  residues processed: 55
  average time/residue: 0.0532
  time to fit residues: 3.6030
Evaluate side-chains
  53 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  528 THR
Chi-restraints excluded: chain K residue  572 LEU
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  593 PHE
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  678 SER
Chi-restraints excluded: chain K residue  699 VAL
Chi-restraints excluded: chain K residue  706 MET
Chi-restraints excluded: chain K residue  750 ASP
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.214321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186103 restraints weight = 3592.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.187335 restraints weight = 2724.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.189039 restraints weight = 2066.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.189750 restraints weight = 1717.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.190015 restraints weight = 1383.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2730  Z= 0.157
  Angle     :  0.646   9.544   3683  Z= 0.331
  Chirality :  0.045   0.137    410
  Planarity :  0.004   0.029    468
  Dihedral  :  4.905  16.047    354
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 23.00 %
    Favored  : 70.67 %
  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: -0.82 (0.45), residues: 329
  helix:  0.25 (0.48), residues: 115
  sheet:  0.92 (0.67), residues: 60
  loop : -1.81 (0.46), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 590 
 TYR   0.017   0.002   TYR K 580 
 PHE   0.008   0.001   PHE K 594 
 TRP   0.021   0.003   TRP K 577 
 HIS   0.003   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2730)
  covalent geometry    : angle       0.64612 ( 3683)
  hydrogen bonds       : bond        0.04323 (  117)
  hydrogen bonds       : angle       5.26727 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5776 (mt)
REVERT: K  616 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7805 (mtm110)
REVERT: K  672 LYS cc_start: 0.5653 (tppt) cc_final: 0.4603 (ptpt)
  outliers start: 19
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0737
  time to fit residues: 4.6297
Evaluate side-chains
  49 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  528 THR
Chi-restraints excluded: chain K residue  572 LEU
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  616 ARG
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  660 THR
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  750 ASP
Chi-restraints excluded: chain K residue  760 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
K 525 HIS
K 563 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.209459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181823 restraints weight = 3625.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.182640 restraints weight = 2863.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.184801 restraints weight = 2080.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.185489 restraints weight = 1751.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.185714 restraints weight = 1360.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2730  Z= 0.205
  Angle     :  0.709  11.036   3683  Z= 0.365
  Chirality :  0.048   0.137    410
  Planarity :  0.005   0.040    468
  Dihedral  :  5.311  17.966    354
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 24.67 %
    Favored  : 67.33 %
  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: -1.06 (0.45), residues: 329
  helix:  0.13 (0.48), residues: 116
  sheet:  0.73 (0.68), residues: 60
  loop : -2.02 (0.45), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 648 
 TYR   0.018   0.002   TYR K 580 
 PHE   0.013   0.002   PHE K 593 
 TRP   0.024   0.004   TRP K 577 
 HIS   0.004   0.001   HIS K 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 2730)
  covalent geometry    : angle       0.70899 ( 3683)
  hydrogen bonds       : bond        0.05012 (  117)
  hydrogen bonds       : angle       5.51808 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 41
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5833 (mt)
REVERT: K  616 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (mtp-110)
REVERT: K  672 LYS cc_start: 0.5785 (tppt) cc_final: 0.4771 (ptpt)
REVERT: K  745 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6159 (mm)
REVERT: K  779 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6577 (mtp-110)
  outliers start: 24
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0629
  time to fit residues: 4.6042
Evaluate side-chains
  57 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  524 SER
Chi-restraints excluded: chain K residue  528 THR
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  572 LEU
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  593 PHE
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  616 ARG
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  660 THR
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  698 ILE
Chi-restraints excluded: chain K residue  699 VAL
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS
K 651 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.207437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.180851 restraints weight = 3634.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.181156 restraints weight = 2648.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.183656 restraints weight = 2009.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.183947 restraints weight = 1808.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.184369 restraints weight = 1427.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2730  Z= 0.197
  Angle     :  0.688  10.398   3683  Z= 0.357
  Chirality :  0.047   0.134    410
  Planarity :  0.005   0.038    468
  Dihedral  :  5.288  17.570    354
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 26.33 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.44), residues: 329
  helix:  0.01 (0.48), residues: 116
  sheet:  0.50 (0.68), residues: 60
  loop : -2.11 (0.44), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 648 
 TYR   0.018   0.002   TYR K 580 
 PHE   0.017   0.002   PHE K 594 
 TRP   0.022   0.004   TRP K 577 
 HIS   0.003   0.001   HIS K 794 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 2730)
  covalent geometry    : angle       0.68829 ( 3683)
  hydrogen bonds       : bond        0.04823 (  117)
  hydrogen bonds       : angle       5.49451 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5868 (mt)
REVERT: K  672 LYS cc_start: 0.5787 (tppt) cc_final: 0.4754 (ptpt)
REVERT: K  745 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6124 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 57
  average time/residue: 0.0688
  time to fit residues: 4.7009
Evaluate side-chains
  54 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  524 SER
Chi-restraints excluded: chain K residue  528 THR
Chi-restraints excluded: chain K residue  533 LEU
Chi-restraints excluded: chain K residue  546 SER
Chi-restraints excluded: chain K residue  572 LEU
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  593 PHE
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  660 THR
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  698 ILE
Chi-restraints excluded: chain K residue  721 ILE
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0870
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0980
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0770
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.1716

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.215298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.189500 restraints weight = 3620.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.190288 restraints weight = 2484.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.192662 restraints weight = 1814.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.193122 restraints weight = 1534.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.193314 restraints weight = 1237.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2730  Z= 0.103
  Angle     :  0.558   7.908   3683  Z= 0.285
  Chirality :  0.042   0.120    410
  Planarity :  0.004   0.039    468
  Dihedral  :  4.578  15.694    354
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 27.67 %
    Favored  : 67.33 %
  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: -0.84 (0.46), residues: 329
  helix:  0.26 (0.50), residues: 115
  sheet:  0.98 (0.71), residues: 59
  loop : -1.87 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 779 
 TYR   0.016   0.001   TYR K 580 
 PHE   0.007   0.001   PHE K 499 
 TRP   0.019   0.002   TRP K 577 
 HIS   0.004   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 2730)
  covalent geometry    : angle       0.55830 ( 3683)
  hydrogen bonds       : bond        0.03430 (  117)
  hydrogen bonds       : angle       4.88035 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6293 (mp) cc_final: 0.5830 (mt)
REVERT: K  577 TRP cc_start: 0.5654 (t60) cc_final: 0.5398 (t60)
REVERT: K  672 LYS cc_start: 0.5677 (tppt) cc_final: 0.4582 (ptpt)
REVERT: K  745 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6091 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 52
  average time/residue: 0.0558
  time to fit residues: 3.6023
Evaluate side-chains
  48 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  678 SER
Chi-restraints excluded: chain K residue  721 ILE
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 18 optimal weight:    0.0030
   chunk 23 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 5 optimal weight:    0.4980
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.212328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186258 restraints weight = 3713.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.186966 restraints weight = 2453.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.189622 restraints weight = 1779.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.190176 restraints weight = 1449.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.190245 restraints weight = 1200.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2730  Z= 0.125
  Angle     :  0.594   9.054   3683  Z= 0.299
  Chirality :  0.043   0.132    410
  Planarity :  0.004   0.036    468
  Dihedral  :  4.547  15.081    354
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 27.67 %
    Favored  : 67.33 %
  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: -0.81 (0.46), residues: 329
  helix:  0.26 (0.50), residues: 114
  sheet:  1.02 (0.71), residues: 59
  loop : -1.82 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 779 
 TYR   0.014   0.001   TYR K 580 
 PHE   0.016   0.001   PHE K 711 
 TRP   0.015   0.002   TRP K 577 
 HIS   0.005   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2730)
  covalent geometry    : angle       0.59373 ( 3683)
  hydrogen bonds       : bond        0.03770 (  117)
  hydrogen bonds       : angle       4.88312 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6290 (mp) cc_final: 0.5808 (mt)
REVERT: K  577 TRP cc_start: 0.5640 (t60) cc_final: 0.5354 (t60)
REVERT: K  672 LYS cc_start: 0.5876 (tppt) cc_final: 0.4718 (ptpt)
REVERT: K  745 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6086 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0471
  time to fit residues: 3.0614
Evaluate side-chains
  50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  524 SER
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  678 SER
Chi-restraints excluded: chain K residue  698 ILE
Chi-restraints excluded: chain K residue  721 ILE
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0050
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.216400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.191000 restraints weight = 3738.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.194660 restraints weight = 2512.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.195790 restraints weight = 1639.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.196116 restraints weight = 1263.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.196127 restraints weight = 1170.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2730  Z= 0.119
  Angle     :  0.597   8.885   3683  Z= 0.294
  Chirality :  0.043   0.131    410
  Planarity :  0.004   0.037    468
  Dihedral  :  4.490  14.709    354
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.33 %
    Favored  : 67.67 %
  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: -0.74 (0.46), residues: 329
  helix:  0.26 (0.50), residues: 114
  sheet:  1.13 (0.72), residues: 59
  loop : -1.77 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 779 
 TYR   0.014   0.001   TYR K 580 
 PHE   0.018   0.001   PHE K 711 
 TRP   0.016   0.002   TRP K 577 
 HIS   0.005   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2730)
  covalent geometry    : angle       0.59688 ( 3683)
  hydrogen bonds       : bond        0.03590 (  117)
  hydrogen bonds       : angle       4.81668 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6260 (mp) cc_final: 0.5761 (mt)
REVERT: K  577 TRP cc_start: 0.5688 (t60) cc_final: 0.5403 (t60)
REVERT: K  672 LYS cc_start: 0.5826 (tppt) cc_final: 0.4739 (ptpt)
REVERT: K  745 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6163 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 50
  average time/residue: 0.0565
  time to fit residues: 3.4522
Evaluate side-chains
  49 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  524 SER
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  678 SER
Chi-restraints excluded: chain K residue  698 ILE
Chi-restraints excluded: chain K residue  721 ILE
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0030
   chunk 20 optimal weight:    0.0470
   chunk 13 optimal weight:    0.3980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3088

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.217238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.189971 restraints weight = 3681.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.193499 restraints weight = 2237.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.195700 restraints weight = 1605.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.196929 restraints weight = 1296.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.198051 restraints weight = 1142.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2730  Z= 0.120
  Angle     :  0.591   8.702   3683  Z= 0.292
  Chirality :  0.043   0.130    410
  Planarity :  0.004   0.037    468
  Dihedral  :  4.465  14.432    354
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.67 %
    Favored  : 67.33 %
  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: -0.71 (0.47), residues: 329
  helix:  0.28 (0.50), residues: 114
  sheet:  1.09 (0.71), residues: 59
  loop : -1.71 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 779 
 TYR   0.014   0.001   TYR K 580 
 PHE   0.018   0.001   PHE K 711 
 TRP   0.016   0.002   TRP K 577 
 HIS   0.005   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2730)
  covalent geometry    : angle       0.59114 ( 3683)
  hydrogen bonds       : bond        0.03578 (  117)
  hydrogen bonds       : angle       4.83020 (  333)

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

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

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  658 Ramachandran restraints generated.
    329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  572 LEU cc_start: 0.6277 (mp) cc_final: 0.5771 (mt)
REVERT: K  577 TRP cc_start: 0.5853 (t60) cc_final: 0.5587 (t60)
REVERT: K  672 LYS cc_start: 0.5790 (tppt) cc_final: 0.4726 (ptpt)
REVERT: K  745 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6190 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 46
  average time/residue: 0.0435
  time to fit residues: 2.5411
Evaluate side-chains
  47 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  510 ILE
Chi-restraints excluded: chain K residue  524 SER
Chi-restraints excluded: chain K residue  579 HIS
Chi-restraints excluded: chain K residue  604 GLU
Chi-restraints excluded: chain K residue  629 LEU
Chi-restraints excluded: chain K residue  669 LEU
Chi-restraints excluded: chain K residue  678 SER
Chi-restraints excluded: chain K residue  698 ILE
Chi-restraints excluded: chain K residue  721 ILE
Chi-restraints excluded: chain K residue  745 LEU
Chi-restraints excluded: chain K residue  750 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
K 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.211999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.186574 restraints weight = 3704.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.188310 restraints weight = 2381.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.191247 restraints weight = 1660.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.191600 restraints weight = 1286.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.192948 restraints weight = 1197.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2730  Z= 0.180
  Angle     :  0.689  10.081   3683  Z= 0.345
  Chirality :  0.046   0.136    410
  Planarity :  0.004   0.037    468
  Dihedral  :  4.989  16.695    354
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 28.67 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.46), residues: 329
  helix:  0.04 (0.49), residues: 116
  sheet:  0.95 (0.69), residues: 59
  loop : -2.02 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 616 
 TYR   0.014   0.002   TYR K 580 
 PHE   0.017   0.002   PHE K 711 
 TRP   0.015   0.003   TRP K 577 
 HIS   0.008   0.001   HIS K 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 2730)
  covalent geometry    : angle       0.68900 ( 3683)
  hydrogen bonds       : bond        0.04544 (  117)
  hydrogen bonds       : angle       5.20192 (  333)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 754.41 seconds
wall clock time: 13 minutes 42.62 seconds (822.62 seconds total)