Starting phenix.real_space_refine
on Fri Aug 22 13:38:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8drq_27681/08_2025/8drq_27681.map"
  }
  resolution = 4.16
  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=   0.001 sd=   0.045
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       8      5.16       5
     C    2135      2.51       5
     N     583      2.21       5
     O     595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 3321
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
  Time building chain proxies: 1.16, per 1000 atoms: 0.35
  Number of scatterers: 3321
  At special positions: 0
  Unit cell: (75.456, 81.744, 78.6, 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       8     16.00
     O     595      8.00
     N     583      7.00
     C    2135      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: 0.26
  Conformation dependent library (CDL) restraints added in 128.5 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      31.4% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'E' and resid 402 through 411
    Processing helix  chain 'E' and resid 412 through 420
    Processing helix  chain 'E' and resid 439 through 444
      removed outlier: 3.790A  pdb=" N   PHE E 443 " --> pdb=" O   PRO E 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 462 through 468
      removed outlier: 3.589A  pdb=" N   ILE E 465 " --> pdb=" O   PRO E 462 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 484 through 494
    Processing helix  chain 'E' and resid 510 through 514
      removed outlier: 4.056A  pdb=" N   TYR E 513 " --> pdb=" O   LEU E 510 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 537 through 541
      removed outlier: 3.702A  pdb=" N   ARG E 541 " --> pdb=" O   ASP E 538 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 559 through 566
      removed outlier: 3.788A  pdb=" N   THR E 563 " --> pdb=" O   PRO E 559 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 632 through 638
      removed outlier: 3.750A  pdb=" N   GLN E 636 " --> pdb=" O   ILE E 633 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   HIS E 637 " --> pdb=" O   SER E 634 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 655 through 661
      removed outlier: 3.525A  pdb=" N   LEU E 661 " --> pdb=" O   ILE E 658 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 679 through 684
      removed outlier: 3.647A  pdb=" N   CYS E 684 " --> pdb=" O   LEU E 681 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 701 through 707
      removed outlier: 3.953A  pdb=" N   ILE E 704 " --> pdb=" O   PRO E 701 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU E 707 " --> pdb=" O   ILE E 704 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 724 through 730
      removed outlier: 3.629A  pdb=" N   PHE E 728 " --> pdb=" O   PRO E 724 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS E 730 " --> pdb=" O   GLU E 726 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 747 through 753
    Processing helix  chain 'E' and resid 771 through 776
      removed outlier: 3.560A  pdb=" N   CYS E 776 " --> pdb=" O   GLU E 772 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 788 through 793
    Processing helix  chain 'E' and resid 795 through 808
    Processing sheet with id=AA1, first strand: chain 'E' and resid 421 through 422
      removed outlier: 6.410A  pdb=" N   LEU E 428 " --> pdb=" O   VAL E 450 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   LYS E 452 " --> pdb=" O   LEU E 428 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU E 430 " --> pdb=" O   LYS E 452 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   GLU E 454 " --> pdb=" O   LEU E 430 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   LEU E 432 " --> pdb=" O   GLU E 454 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LEU E 474 " --> pdb=" O   HIS E 499 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   LYS E 501 " --> pdb=" O   LEU E 474 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   LEU E 476 " --> pdb=" O   LYS E 501 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU E 498 " --> pdb=" O   HIS E 522 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   THR E 524 " --> pdb=" O   LEU E 498 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE E 500 " --> pdb=" O   THR E 524 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LEU E 572 " --> pdb=" O   GLU E 597 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ILE E 599 " --> pdb=" O   LEU E 572 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ILE E 574 " --> pdb=" O   ILE E 599 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU E 596 " --> pdb=" O   GLU E 618 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASP E 620 " --> pdb=" O   LEU E 596 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU E 598 " --> pdb=" O   ASP E 620 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 459 through 460
      removed outlier: 6.483A  pdb=" N   VAL E 459 " --> pdb=" O   LYS E 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'E' and resid 666 through 668
      removed outlier: 6.334A  pdb=" N   TYR E 689 " --> pdb=" O   LEU E 667 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU E 690 " --> pdb=" O   ALA E 714 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ILE E 759 " --> pdb=" O   VAL E 785 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    159 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: 0.46

  Time building geometry restraints manager: 0.36 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: 1098
        1.34 -     1.46: 490
        1.46 -     1.58: 1779
        1.58 -     1.69: 1
        1.69 -     1.81: 10
  Bond restraints: 3378
  Sorted by residual:
  bond pdb=" N   PRO E 678 "
       pdb=" CD  PRO E 678 "
    ideal  model  delta    sigma   weight residual
    1.473  1.417  0.056 1.40e-02 5.10e+03 1.59e+01
  bond pdb=" CB  PRO E 678 "
       pdb=" CG  PRO E 678 "
    ideal  model  delta    sigma   weight residual
    1.492  1.614 -0.122 5.00e-02 4.00e+02 5.92e+00
  bond pdb=" CB  ASN E 712 "
       pdb=" CG  ASN E 712 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.36e+00
  bond pdb=" CG  PRO E 678 "
       pdb=" CD  PRO E 678 "
    ideal  model  delta    sigma   weight residual
    1.503  1.460  0.043 3.40e-02 8.65e+02 1.57e+00
  bond pdb=" N   TYR E 534 "
       pdb=" CA  TYR E 534 "
    ideal  model  delta    sigma   weight residual
    1.459  1.471 -0.012 1.15e-02 7.56e+03 1.15e+00
  ... (remaining 3373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 4412
        2.03 -     4.06: 140
        4.06 -     6.10: 20
        6.10 -     8.13: 7
        8.13 -    10.16: 1
  Bond angle restraints: 4580
  Sorted by residual:
  angle pdb=" CA  MET E 590 "
        pdb=" CB  MET E 590 "
        pdb=" CG  MET E 590 "
      ideal   model   delta    sigma   weight residual
     114.10  121.55   -7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" CB  MET E 590 "
        pdb=" CG  MET E 590 "
        pdb=" SD  MET E 590 "
      ideal   model   delta    sigma   weight residual
     112.70  122.86  -10.16 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" C   ASN E 712 "
        pdb=" CA  ASN E 712 "
        pdb=" CB  ASN E 712 "
      ideal   model   delta    sigma   weight residual
     109.38  115.03   -5.65 1.80e+00 3.09e-01 9.85e+00
  angle pdb=" N   PRO E 678 "
        pdb=" CD  PRO E 678 "
        pdb=" CG  PRO E 678 "
      ideal   model   delta    sigma   weight residual
     103.20  107.80   -4.60 1.50e+00 4.44e-01 9.42e+00
  angle pdb=" C   LEU E 603 "
        pdb=" N   GLU E 604 "
        pdb=" CA  GLU E 604 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.02e+00
  ... (remaining 4575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.43: 1759
       15.43 -    30.85: 250
       30.85 -    46.28: 67
       46.28 -    61.70: 17
       61.70 -    77.13: 1
  Dihedral angle restraints: 2094
    sinusoidal: 892
      harmonic: 1202
  Sorted by residual:
  dihedral pdb=" CA  LEU E 468 "
           pdb=" C   LEU E 468 "
           pdb=" N   THR E 469 "
           pdb=" CA  THR E 469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.19  -23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  ILE E 535 "
           pdb=" C   ILE E 535 "
           pdb=" N   VAL E 536 "
           pdb=" CA  VAL E 536 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.51   22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  THR E 662 "
           pdb=" C   THR E 662 "
           pdb=" N   ASN E 663 "
           pdb=" CA  ASN E 663 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.50  -19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 2091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 316
       0.036 -    0.071: 163
       0.071 -    0.107: 53
       0.107 -    0.143: 15
       0.143 -    0.178: 2
  Chirality restraints: 549
  Sorted by residual:
  chirality pdb=" CB  VAL E 786 "
            pdb=" CA  VAL E 786 "
            pdb=" CG1 VAL E 786 "
            pdb=" CG2 VAL E 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  VAL E 786 "
            pdb=" N   VAL E 786 "
            pdb=" C   VAL E 786 "
            pdb=" CB  VAL E 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  ILE E 654 "
            pdb=" N   ILE E 654 "
            pdb=" C   ILE E 654 "
            pdb=" CB  ILE E 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 546 not shown)

  Planarity restraints: 578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 677 "   -0.047 5.00e-02 4.00e+02   7.27e-02 8.45e+00
        pdb=" N   PRO E 678 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO E 678 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO E 678 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 490 "   -0.007 2.00e-02 2.50e+03   1.84e-02 5.90e+00
        pdb=" CG  PHE E 490 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 490 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 490 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 490 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 490 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 490 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 746 "    0.030 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO E 747 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO E 747 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 747 "    0.026 5.00e-02 4.00e+02
  ... (remaining 575 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 850
        2.81 -     3.33: 3133
        3.33 -     3.85: 5736
        3.85 -     4.38: 7140
        4.38 -     4.90: 11097
  Nonbonded interactions: 27956
  Sorted by model distance:
  nonbonded pdb=" O   VAL E 591 "
            pdb=" ND2 ASN E 615 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   LEU E 476 "
            pdb=" N   LYS E 501 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OH  TYR E 689 "
            pdb=" OE1 GLN E 711 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLN E 560 "
            pdb=" OG1 THR E 563 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   LEU E 790 "
            pdb=" OG1 THR E 793 "
     model   vdw
     2.329 3.040
  ... (remaining 27951 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             4.910
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.600
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5765
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      :  0.004   0.122   3378  Z= 0.204
  Angle     :  0.891  10.159   4580  Z= 0.486
  Chirality :  0.048   0.178    549
  Planarity :  0.006   0.073    578
  Dihedral  : 15.597  77.126   1306
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.31 %
    Favored  : 80.69 %
  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: -3.30 (0.39), residues: 405
  helix: -3.27 (0.37), residues: 114
  sheet: -2.33 (0.78), residues: 54
  loop : -1.55 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 545 
 TYR   0.012   0.002   TYR E 477 
 PHE   0.039   0.003   PHE E 490 
 TRP   0.031   0.003   TRP E 475 
 HIS   0.011   0.002   HIS E 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3378)
  covalent geometry    : angle       0.89099 ( 4580)
  hydrogen bonds       : bond        0.17348 (   72)
  hydrogen bonds       : angle       8.40474 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  419 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8130 (tpt-90)
REVERT: E  458 ASP cc_start: 0.7150 (m-30) cc_final: 0.6770 (t0)
REVERT: E  465 ILE cc_start: 0.9158 (tt) cc_final: 0.8907 (tt)
REVERT: E  474 LEU cc_start: 0.8956 (tt) cc_final: 0.8426 (tt)
REVERT: E  496 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8046 (mpt180)
REVERT: E  507 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5197 (mt-10)
REVERT: E  520 GLU cc_start: 0.8635 (tt0) cc_final: 0.8389 (tt0)
REVERT: E  555 LEU cc_start: 0.7678 (tp) cc_final: 0.7448 (tp)
REVERT: E  581 LEU cc_start: 0.7922 (mp) cc_final: 0.7232 (tt)
REVERT: E  592 ASN cc_start: 0.8192 (m-40) cc_final: 0.7941 (m110)
REVERT: E  650 HIS cc_start: 0.6995 (m-70) cc_final: 0.6632 (m-70)
REVERT: E  723 LEU cc_start: 0.5309 (mt) cc_final: 0.4532 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1167
  time to fit residues: 18.7589
Evaluate side-chains
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.1980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
E 711 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.139541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.125369 restraints weight = 16666.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.127180 restraints weight = 12235.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.128652 restraints weight = 9394.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.129615 restraints weight = 7440.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.130399 restraints weight = 6193.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5581
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3378  Z= 0.167
  Angle     :  0.782  10.697   4580  Z= 0.375
  Chirality :  0.049   0.180    549
  Planarity :  0.007   0.058    578
  Dihedral  :  5.767  18.550    439
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 23.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.29 %
    Favored  : 94.44 %
  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: -3.84 (0.37), residues: 405
  helix: -3.03 (0.35), residues: 141
  sheet: -2.55 (0.69), residues: 58
  loop : -2.10 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 541 
 TYR   0.029   0.004   TYR E 668 
 PHE   0.015   0.002   PHE E 490 
 TRP   0.039   0.004   TRP E 647 
 HIS   0.018   0.003   HIS E 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3378)
  covalent geometry    : angle       0.78232 ( 4580)
  hydrogen bonds       : bond        0.04629 (   72)
  hydrogen bonds       : angle       6.71173 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  521 LEU cc_start: 0.8231 (tt) cc_final: 0.7903 (mt)
REVERT: E  555 LEU cc_start: 0.6659 (tp) cc_final: 0.6423 (tp)
REVERT: E  592 ASN cc_start: 0.8004 (m-40) cc_final: 0.7790 (m110)
REVERT: E  640 ARG cc_start: 0.4848 (mpp-170) cc_final: 0.3748 (mmp-170)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1031
  time to fit residues: 12.8613
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0050
   overall best weight:    0.4572

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

Flipped N/Q/H residues before XYZ refinement:
E 694 HIS
E 741 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.138658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.124686 restraints weight = 15731.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.127005 restraints weight = 10839.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.128771 restraints weight = 7769.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.129914 restraints weight = 5848.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.130863 restraints weight = 4645.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.4425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5523
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3378  Z= 0.120
  Angle     :  0.659   7.321   4580  Z= 0.320
  Chirality :  0.044   0.142    549
  Planarity :  0.004   0.037    578
  Dihedral  :  5.187  17.409    439
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  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: -3.50 (0.39), residues: 405
  helix: -2.84 (0.39), residues: 135
  sheet: -1.94 (0.81), residues: 50
  loop : -2.05 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 666 
 TYR   0.018   0.002   TYR E 477 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.037   0.003   TRP E 647 
 HIS   0.008   0.001   HIS E 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3378)
  covalent geometry    : angle       0.65875 ( 4580)
  hydrogen bonds       : bond        0.03877 (   72)
  hydrogen bonds       : angle       6.14452 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  473 GLU cc_start: 0.4793 (tp30) cc_final: 0.4541 (tp30)
REVERT: E  521 LEU cc_start: 0.8288 (tt) cc_final: 0.7902 (mt)
REVERT: E  640 ARG cc_start: 0.4480 (mpp-170) cc_final: 0.3423 (mmp-170)
REVERT: E  685 ARG cc_start: 0.6529 (mmp-170) cc_final: 0.5644 (tpt-90)
REVERT: E  732 LYS cc_start: 0.6413 (tptp) cc_final: 0.5733 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0830
  time to fit residues: 9.8897
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0370
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
E 694 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.140185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.126672 restraints weight = 16780.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.128546 restraints weight = 12137.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.129819 restraints weight = 9172.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.131041 restraints weight = 7319.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.131663 restraints weight = 6022.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5492
moved from start:          0.6259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3378  Z= 0.119
  Angle     :  0.680   8.265   4580  Z= 0.322
  Chirality :  0.046   0.176    549
  Planarity :  0.005   0.069    578
  Dihedral  :  5.048  15.664    439
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  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: -3.39 (0.39), residues: 405
  helix: -2.72 (0.40), residues: 131
  sheet: -2.07 (0.72), residues: 56
  loop : -1.95 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 762 
 TYR   0.012   0.002   TYR E 653 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.036   0.003   TRP E 647 
 HIS   0.005   0.001   HIS E 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3378)
  covalent geometry    : angle       0.67980 ( 4580)
  hydrogen bonds       : bond        0.03240 (   72)
  hydrogen bonds       : angle       5.58660 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  640 ARG cc_start: 0.4451 (mpp-170) cc_final: 0.3480 (mmp-170)
REVERT: E  685 ARG cc_start: 0.6233 (mmp-170) cc_final: 0.5743 (tpt170)
REVERT: E  732 LYS cc_start: 0.6806 (tptp) cc_final: 0.6553 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0932
  time to fit residues: 9.8138
Evaluate side-chains
  66 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
E 554 ASN
E 755 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.134543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.121955 restraints weight = 15573.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.123698 restraints weight = 11441.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.125190 restraints weight = 8909.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.126120 restraints weight = 7345.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.126942 restraints weight = 6188.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5804
moved from start:          0.7409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3378  Z= 0.187
  Angle     :  0.835  10.439   4580  Z= 0.398
  Chirality :  0.049   0.155    549
  Planarity :  0.006   0.048    578
  Dihedral  :  5.909  20.380    439
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 25.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.97 %
    Favored  : 95.77 %
  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: -3.61 (0.38), residues: 405
  helix: -2.89 (0.39), residues: 123
  sheet: -1.89 (0.77), residues: 50
  loop : -2.25 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 688 
 TYR   0.013   0.002   TYR E 683 
 PHE   0.014   0.003   PHE E 728 
 TRP   0.041   0.004   TRP E 647 
 HIS   0.006   0.002   HIS E 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3378)
  covalent geometry    : angle       0.83488 ( 4580)
  hydrogen bonds       : bond        0.03948 (   72)
  hydrogen bonds       : angle       6.31873 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  423 ASN cc_start: 0.7169 (p0) cc_final: 0.6851 (p0)
REVERT: E  532 ASN cc_start: 0.4891 (m-40) cc_final: 0.4468 (m-40)
REVERT: E  729 GLN cc_start: 0.4730 (mp10) cc_final: 0.2940 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0847
  time to fit residues: 9.2458
Evaluate side-chains
  68 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.135950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.123517 restraints weight = 16713.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.125338 restraints weight = 11705.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.126829 restraints weight = 8777.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.127714 restraints weight = 6967.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.128469 restraints weight = 5772.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5705
moved from start:          0.7809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3378  Z= 0.128
  Angle     :  0.713   6.617   4580  Z= 0.344
  Chirality :  0.046   0.143    549
  Planarity :  0.005   0.036    578
  Dihedral  :  5.349  18.677    439
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  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: -3.50 (0.38), residues: 405
  helix: -2.76 (0.40), residues: 129
  sheet: -1.94 (0.73), residues: 48
  loop : -2.15 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 640 
 TYR   0.008   0.002   TYR E 668 
 PHE   0.016   0.002   PHE E 443 
 TRP   0.038   0.004   TRP E 647 
 HIS   0.004   0.001   HIS E 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3378)
  covalent geometry    : angle       0.71339 ( 4580)
  hydrogen bonds       : bond        0.03272 (   72)
  hydrogen bonds       : angle       5.96285 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  452 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7783 (ttmm)
REVERT: E  532 ASN cc_start: 0.4717 (m-40) cc_final: 0.4371 (m-40)
REVERT: E  640 ARG cc_start: 0.4205 (mpp-170) cc_final: 0.2986 (tpp-160)
REVERT: E  685 ARG cc_start: 0.5853 (tpp-160) cc_final: 0.5106 (tpt170)
REVERT: E  729 GLN cc_start: 0.4549 (mp10) cc_final: 0.3264 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0830
  time to fit residues: 8.4572
Evaluate side-chains
  65 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** E 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 694 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.135860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.122768 restraints weight = 17097.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.124600 restraints weight = 12115.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.125974 restraints weight = 9103.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.126868 restraints weight = 7224.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.127733 restraints weight = 6012.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5687
moved from start:          0.8114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3378  Z= 0.125
  Angle     :  0.706   6.807   4580  Z= 0.341
  Chirality :  0.045   0.132    549
  Planarity :  0.005   0.040    578
  Dihedral  :  5.147  16.453    439
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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: -3.31 (0.39), residues: 405
  helix: -2.54 (0.42), residues: 123
  sheet: -1.99 (0.70), residues: 48
  loop : -2.06 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 545 
 TYR   0.009   0.001   TYR E 683 
 PHE   0.011   0.002   PHE E 433 
 TRP   0.040   0.004   TRP E 647 
 HIS   0.005   0.001   HIS E 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3378)
  covalent geometry    : angle       0.70636 ( 4580)
  hydrogen bonds       : bond        0.03356 (   72)
  hydrogen bonds       : angle       5.94421 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  434 MET cc_start: 0.5538 (mmp) cc_final: 0.5183 (mmp)
REVERT: E  532 ASN cc_start: 0.4831 (m-40) cc_final: 0.4447 (m-40)
REVERT: E  729 GLN cc_start: 0.4649 (mp10) cc_final: 0.4248 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0718
  time to fit residues: 7.0799
Evaluate side-chains
  62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.0170
   chunk 20 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
E 694 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.137833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.124186 restraints weight = 17068.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.125981 restraints weight = 12153.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.127351 restraints weight = 9198.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.128250 restraints weight = 7327.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.129121 restraints weight = 6154.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5672
moved from start:          0.8313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3378  Z= 0.112
  Angle     :  0.685   7.169   4580  Z= 0.329
  Chirality :  0.044   0.136    549
  Planarity :  0.004   0.034    578
  Dihedral  :  4.971  20.784    439
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  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: -3.25 (0.38), residues: 405
  helix: -2.47 (0.42), residues: 124
  sheet: -2.18 (0.69), residues: 50
  loop : -1.97 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 671 
 TYR   0.012   0.001   TYR E 668 
 PHE   0.038   0.002   PHE E 433 
 TRP   0.038   0.004   TRP E 647 
 HIS   0.007   0.001   HIS E 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3378)
  covalent geometry    : angle       0.68500 ( 4580)
  hydrogen bonds       : bond        0.03156 (   72)
  hydrogen bonds       : angle       5.73465 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  434 MET cc_start: 0.5856 (mmp) cc_final: 0.5471 (mmp)
REVERT: E  452 LYS cc_start: 0.7490 (ttpt) cc_final: 0.6497 (ttmm)
REVERT: E  532 ASN cc_start: 0.4952 (m-40) cc_final: 0.4597 (m-40)
REVERT: E  597 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6343 (mm-30)
REVERT: E  729 GLN cc_start: 0.4583 (mp10) cc_final: 0.4249 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0599
  time to fit residues: 6.1490
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0060
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0470
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.2652

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

Flipped N/Q/H residues before XYZ refinement:
E 694 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.138817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.125442 restraints weight = 17222.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.127166 restraints weight = 12359.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.128542 restraints weight = 9394.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.129513 restraints weight = 7502.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.130126 restraints weight = 6274.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5606
moved from start:          0.8517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3378  Z= 0.109
  Angle     :  0.665   7.160   4580  Z= 0.316
  Chirality :  0.045   0.140    549
  Planarity :  0.004   0.042    578
  Dihedral  :  4.752  17.459    439
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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: -3.19 (0.39), residues: 405
  helix: -2.35 (0.44), residues: 123
  sheet: -2.15 (0.69), residues: 50
  loop : -1.97 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 541 
 TYR   0.005   0.001   TYR E 513 
 PHE   0.024   0.002   PHE E 433 
 TRP   0.040   0.005   TRP E 475 
 HIS   0.004   0.001   HIS E 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3378)
  covalent geometry    : angle       0.66542 ( 4580)
  hydrogen bonds       : bond        0.03065 (   72)
  hydrogen bonds       : angle       5.64385 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  532 ASN cc_start: 0.4895 (m-40) cc_final: 0.4548 (m-40)
REVERT: E  737 HIS cc_start: 0.6559 (m90) cc_final: 0.6341 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0754
  time to fit residues: 7.8235
Evaluate side-chains
  62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0970
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 26 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** E 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 694 HIS
E 708 GLN
E 711 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.137781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.124245 restraints weight = 17289.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.126028 restraints weight = 12406.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.127367 restraints weight = 9455.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.128163 restraints weight = 7577.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.129135 restraints weight = 6425.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5649
moved from start:          0.8889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3378  Z= 0.125
  Angle     :  0.729   7.748   4580  Z= 0.348
  Chirality :  0.047   0.201    549
  Planarity :  0.005   0.039    578
  Dihedral  :  5.015  19.381    439
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.17 (0.38), residues: 405
  helix: -2.42 (0.43), residues: 118
  sheet: -1.94 (0.74), residues: 45
  loop : -2.00 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 688 
 TYR   0.013   0.001   TYR E 668 
 PHE   0.019   0.003   PHE E 728 
 TRP   0.038   0.005   TRP E 411 
 HIS   0.005   0.001   HIS E 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3378)
  covalent geometry    : angle       0.72940 ( 4580)
  hydrogen bonds       : bond        0.03518 (   72)
  hydrogen bonds       : angle       5.62065 (  159)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  532 ASN cc_start: 0.4815 (m-40) cc_final: 0.4471 (m-40)
REVERT: E  737 HIS cc_start: 0.6645 (m90) cc_final: 0.6366 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0763
  time to fit residues: 7.6775
Evaluate side-chains
  61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.0370
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0050
   chunk 13 optimal weight:    0.0370
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.3952

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

Flipped N/Q/H residues before XYZ refinement:
E 694 HIS
E 708 GLN
E 711 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.139568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.128415 restraints weight = 17811.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.130106 restraints weight = 12478.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.131389 restraints weight = 9280.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.131979 restraints weight = 7312.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 70)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.133246 restraints weight = 6195.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5521
moved from start:          0.9039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3378  Z= 0.118
  Angle     :  0.712   9.598   4580  Z= 0.340
  Chirality :  0.047   0.166    549
  Planarity :  0.004   0.037    578
  Dihedral  :  4.892  16.358    439
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.01 (0.38), residues: 405
  helix: -2.43 (0.44), residues: 112
  sheet: -1.98 (0.73), residues: 48
  loop : -1.80 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 666 
 TYR   0.005   0.001   TYR E 513 
 PHE   0.017   0.003   PHE E 728 
 TRP   0.039   0.004   TRP E 411 
 HIS   0.004   0.001   HIS E 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3378)
  covalent geometry    : angle       0.71186 ( 4580)
  hydrogen bonds       : bond        0.03588 (   72)
  hydrogen bonds       : angle       5.68865 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1131.00 seconds
wall clock time: 20 minutes 11.39 seconds (1211.39 seconds total)