Starting phenix.real_space_refine
on Tue Feb 11 00:30:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8drq_27681/02_2025/8drq_27681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8drq_27681/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8drq_27681/02_2025/8drq_27681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8drq_27681/02_2025/8drq_27681.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8drq_27681/02_2025/8drq_27681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8drq_27681/02_2025/8drq_27681.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.52, per 1000 atoms: 1.06
  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: 0.79
  Conformation dependent library (CDL) restraints added in 399.4 milliseconds
  

  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: 0.38
  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: 0.84

  Time building geometry restraints manager: 0.93 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:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.480
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.930
-------------------------------------------------------------------------------
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= 0.295
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.031   0.003   TRP E 475 
 HIS   0.011   0.002   HIS E 694 
 PHE   0.039   0.003   PHE E 490 
 TYR   0.012   0.002   TYR E 477 
 ARG   0.003   0.000   ARG E 545 

*********************** 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  : 0.299 
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: 0.2447
  time to fit residues: 39.3069
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  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 36 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4547 r_free = 0.4547 target = 0.141126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.126819 restraints weight = 16265.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.128614 restraints weight = 11881.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.130015 restraints weight = 9079.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5512
moved from start:          0.4683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3378  Z= 0.215
  Angle     :  0.749  10.661   4580  Z= 0.359
  Chirality :  0.048   0.191    549
  Planarity :  0.006   0.060    578
  Dihedral  :  5.664  18.617    439
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 21.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.56 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.37), residues: 405
  helix: -2.99 (0.36), residues: 141
  sheet: -2.56 (0.69), residues: 58
  loop : -2.10 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.006   TRP E 647 
 HIS   0.017   0.003   HIS E 499 
 PHE   0.017   0.002   PHE E 490 
 TYR   0.034   0.004   TYR E 668 
 ARG   0.008   0.001   ARG E 541 

*********************** 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
  113 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.368 
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: symmetry clash
REVERT: E  507 GLU cc_start: 0.5478 (mt-10) cc_final: 0.5216 (mt-10)
REVERT: E  521 LEU cc_start: 0.8208 (tt) cc_final: 0.7868 (mt)
REVERT: E  555 LEU cc_start: 0.6679 (tp) cc_final: 0.6447 (tp)
REVERT: E  592 ASN cc_start: 0.8020 (m-40) cc_final: 0.7791 (m110)
REVERT: E  603 LEU cc_start: 0.7723 (mt) cc_final: 0.7317 (mt)
REVERT: E  640 ARG cc_start: 0.4835 (mpp-170) cc_final: 0.3675 (mmp-170)
REVERT: E  737 HIS cc_start: 0.7137 (m90) cc_final: 0.6927 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2204
  time to fit residues: 28.5596
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0040
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.0596

-------------------------------------------------------------------------------
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 = 0.4494 r_free = 0.4494 target = 0.137243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.122881 restraints weight = 14435.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.125491 restraints weight = 9661.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.127454 restraints weight = 6861.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5663
moved from start:          0.5746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3378  Z= 0.205
  Angle     :  0.694   6.670   4580  Z= 0.335
  Chirality :  0.045   0.156    549
  Planarity :  0.005   0.060    578
  Dihedral  :  5.306  16.028    439
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.39), residues: 405
  helix: -2.87 (0.38), residues: 128
  sheet: -1.55 (0.83), residues: 48
  loop : -1.94 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP E 647 
 HIS   0.009   0.002   HIS E 522 
 PHE   0.011   0.002   PHE E 490 
 TYR   0.022   0.002   TYR E 477 
 ARG   0.004   0.001   ARG E 666 

*********************** 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  : 0.300 
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: 0.8409 (tt) cc_final: 0.8123 (tp)
REVERT: E  592 ASN cc_start: 0.8136 (m-40) cc_final: 0.7894 (m110)
REVERT: E  640 ARG cc_start: 0.4758 (mpp-170) cc_final: 0.3600 (mmp-170)
REVERT: E  685 ARG cc_start: 0.6681 (mmp-170) cc_final: 0.5839 (tpt-90)
REVERT: E  732 LYS cc_start: 0.6627 (tptp) cc_final: 0.6098 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1795
  time to fit residues: 21.2548
Evaluate side-chains
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.0370
   chunk 33 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   overall best weight:    0.7660

-------------------------------------------------------------------------------
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 = 0.4513 r_free = 0.4513 target = 0.138034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.123557 restraints weight = 14894.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.126134 restraints weight = 10023.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.128080 restraints weight = 7221.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5697
moved from start:          0.6386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3378  Z= 0.177
  Angle     :  0.668   7.456   4580  Z= 0.318
  Chirality :  0.044   0.147    549
  Planarity :  0.005   0.058    578
  Dihedral  :  5.065  16.309    439
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.40), residues: 405
  helix: -2.71 (0.41), residues: 128
  sheet: -1.46 (0.80), residues: 48
  loop : -1.90 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.004   TRP E 647 
 HIS   0.007   0.001   HIS E 522 
 PHE   0.012   0.002   PHE E 490 
 TYR   0.013   0.002   TYR E 668 
 ARG   0.004   0.001   ARG E 666 

*********************** 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  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  443 PHE cc_start: 0.7655 (m-10) cc_final: 0.7245 (m-10)
REVERT: E  521 LEU cc_start: 0.8337 (tt) cc_final: 0.7826 (mt)
REVERT: E  555 LEU cc_start: 0.7035 (tp) cc_final: 0.6795 (tp)
REVERT: E  581 LEU cc_start: 0.7784 (mt) cc_final: 0.7457 (tt)
REVERT: E  592 ASN cc_start: 0.8114 (m-40) cc_final: 0.7854 (m110)
REVERT: E  597 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6747 (tp30)
REVERT: E  640 ARG cc_start: 0.4700 (mpp-170) cc_final: 0.3516 (mmp-170)
REVERT: E  685 ARG cc_start: 0.6545 (mmp-170) cc_final: 0.5848 (tpt170)
REVERT: E  732 LYS cc_start: 0.6755 (tptp) cc_final: 0.6194 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.2016
  time to fit residues: 21.3173
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  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.0770
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.5142

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

Flipped N/Q/H residues before XYZ refinement:
E 554 ASN
E 741 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.138066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.127676 restraints weight = 17177.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.129572 restraints weight = 11519.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.130988 restraints weight = 8195.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
moved from start:          0.7194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3378  Z= 0.218
  Angle     :  0.741   9.078   4580  Z= 0.352
  Chirality :  0.046   0.154    549
  Planarity :  0.005   0.047    578
  Dihedral  :  5.352  17.668    439
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.23 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.40), residues: 405
  helix: -2.79 (0.42), residues: 123
  sheet: -1.56 (0.77), residues: 48
  loop : -1.77 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP E 647 
 HIS   0.007   0.002   HIS E 522 
 PHE   0.011   0.002   PHE E 490 
 TYR   0.007   0.002   TYR E 513 
 ARG   0.003   0.001   ARG E 762 

*********************** 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
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.388 
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  452 LYS cc_start: 0.7483 (mtpt) cc_final: 0.7259 (mtpt)
REVERT: E  473 GLU cc_start: 0.5670 (tp30) cc_final: 0.5079 (tp30)
REVERT: E  521 LEU cc_start: 0.8133 (tt) cc_final: 0.7729 (mt)
REVERT: E  532 ASN cc_start: 0.4562 (m-40) cc_final: 0.4276 (m-40)
REVERT: E  685 ARG cc_start: 0.6258 (mmp-170) cc_final: 0.5715 (tpt170)
REVERT: E  732 LYS cc_start: 0.6423 (tptp) cc_final: 0.6170 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1809
  time to fit residues: 19.1365
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  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0170
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.8224

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.136930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.124486 restraints weight = 16314.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.126551 restraints weight = 11071.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.128086 restraints weight = 8009.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5658
moved from start:          0.7512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3378  Z= 0.180
  Angle     :  0.679   8.861   4580  Z= 0.321
  Chirality :  0.045   0.145    549
  Planarity :  0.004   0.044    578
  Dihedral  :  5.100  16.476    439
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.39), residues: 405
  helix: -2.53 (0.43), residues: 123
  sheet: -1.94 (0.70), residues: 48
  loop : -1.90 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.005   TRP E 647 
 HIS   0.004   0.001   HIS E 522 
 PHE   0.014   0.002   PHE E 433 
 TYR   0.010   0.001   TYR E 668 
 ARG   0.004   0.001   ARG E 640 

*********************** 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
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  469 THR cc_start: 0.7300 (p) cc_final: 0.7095 (p)
REVERT: E  473 GLU cc_start: 0.5229 (tp30) cc_final: 0.4731 (tp30)
REVERT: E  475 TRP cc_start: 0.6839 (m-10) cc_final: 0.6549 (m-10)
REVERT: E  521 LEU cc_start: 0.8159 (tt) cc_final: 0.7871 (mt)
REVERT: E  532 ASN cc_start: 0.4394 (m-40) cc_final: 0.4132 (m-40)
REVERT: E  640 ARG cc_start: 0.4166 (mpp-170) cc_final: 0.2974 (mmp-170)
REVERT: E  685 ARG cc_start: 0.6254 (mmp-170) cc_final: 0.5874 (tpt170)
REVERT: E  732 LYS cc_start: 0.6724 (tptp) cc_final: 0.6418 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1760
  time to fit residues: 18.4974
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  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
E 576 ASN
E 694 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.135600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.122838 restraints weight = 16455.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.124606 restraints weight = 11970.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.126165 restraints weight = 9112.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
moved from start:          0.7906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3378  Z= 0.195
  Angle     :  0.705   8.748   4580  Z= 0.334
  Chirality :  0.046   0.149    549
  Planarity :  0.004   0.042    578
  Dihedral  :  5.090  16.558    439
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.39), residues: 405
  helix: -2.51 (0.44), residues: 117
  sheet: -2.07 (0.69), residues: 48
  loop : -1.83 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP E 411 
 HIS   0.005   0.001   HIS E 694 
 PHE   0.009   0.002   PHE E 611 
 TYR   0.007   0.001   TYR E 683 
 ARG   0.003   0.000   ARG E 671 

*********************** 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
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  532 ASN cc_start: 0.4884 (m-40) cc_final: 0.4412 (m-40)
REVERT: E  640 ARG cc_start: 0.4520 (mpp-170) cc_final: 0.3241 (tpp-160)
REVERT: E  729 GLN cc_start: 0.4610 (mp10) cc_final: 0.4170 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1585
  time to fit residues: 16.3012
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  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.136637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.124443 restraints weight = 16088.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.126242 restraints weight = 11747.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.127553 restraints weight = 8987.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5691
moved from start:          0.8189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3378  Z= 0.171
  Angle     :  0.672   9.151   4580  Z= 0.318
  Chirality :  0.044   0.136    549
  Planarity :  0.005   0.055    578
  Dihedral  :  4.956  15.119    439
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.39), residues: 405
  helix: -2.55 (0.40), residues: 130
  sheet: -2.11 (0.67), residues: 48
  loop : -1.98 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP E 647 
 HIS   0.004   0.001   HIS E 522 
 PHE   0.010   0.001   PHE E 490 
 TYR   0.009   0.002   TYR E 689 
 ARG   0.003   0.000   ARG E 541 

*********************** 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
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  473 GLU cc_start: 0.5453 (tp30) cc_final: 0.4950 (tp30)
REVERT: E  517 THR cc_start: 0.7461 (p) cc_final: 0.7251 (p)
REVERT: E  532 ASN cc_start: 0.4972 (m-40) cc_final: 0.4524 (m-40)
REVERT: E  555 LEU cc_start: 0.6133 (tp) cc_final: 0.5916 (tp)
REVERT: E  640 ARG cc_start: 0.4196 (mpp-170) cc_final: 0.2780 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1653
  time to fit residues: 17.0585
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  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0470
   chunk 19 optimal weight:    7.9990
   chunk 37 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0050
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.3210

-------------------------------------------------------------------------------
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 = 0.4488 r_free = 0.4488 target = 0.137669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.124968 restraints weight = 16672.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.126638 restraints weight = 12262.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.127966 restraints weight = 9524.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5629
moved from start:          0.8371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3378  Z= 0.170
  Angle     :  0.716  10.489   4580  Z= 0.333
  Chirality :  0.045   0.129    549
  Planarity :  0.004   0.044    578
  Dihedral  :  4.927  17.373    439
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.39), residues: 405
  helix: -2.55 (0.40), residues: 130
  sheet: -2.00 (0.71), residues: 48
  loop : -1.91 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP E 411 
 HIS   0.003   0.001   HIS E 522 
 PHE   0.010   0.002   PHE E 490 
 TYR   0.012   0.002   TYR E 689 
 ARG   0.010   0.001   ARG E 688 

*********************** 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
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  473 GLU cc_start: 0.5280 (tp30) cc_final: 0.4953 (tp30)
REVERT: E  532 ASN cc_start: 0.4548 (m-40) cc_final: 0.4194 (m-40)
REVERT: E  555 LEU cc_start: 0.6125 (tp) cc_final: 0.5913 (tp)
REVERT: E  640 ARG cc_start: 0.4211 (mpp-170) cc_final: 0.2816 (tpp-160)
REVERT: E  664 LEU cc_start: 0.6627 (tp) cc_final: 0.5825 (pp)
REVERT: E  729 GLN cc_start: 0.4601 (mp10) cc_final: 0.3127 (tt0)
REVERT: E  732 LYS cc_start: 0.6801 (tptp) cc_final: 0.6355 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1703
  time to fit residues: 18.3406
Evaluate side-chains
  69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.0020
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0570
   chunk 35 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.4306

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.137585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.124960 restraints weight = 16461.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.126691 restraints weight = 12070.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.127969 restraints weight = 9252.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5620
moved from start:          0.8653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3378  Z= 0.196
  Angle     :  0.735  10.375   4580  Z= 0.343
  Chirality :  0.047   0.199    549
  Planarity :  0.005   0.050    578
  Dihedral  :  5.030  22.677    439
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.40), residues: 405
  helix: -2.57 (0.42), residues: 119
  sheet: -1.87 (0.71), residues: 48
  loop : -1.57 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP E 411 
 HIS   0.003   0.001   HIS E 431 
 PHE   0.013   0.002   PHE E 433 
 TYR   0.020   0.002   TYR E 668 
 ARG   0.009   0.001   ARG E 688 

********************** 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
  87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  532 ASN cc_start: 0.4669 (m-40) cc_final: 0.4289 (m-40)
REVERT: E  640 ARG cc_start: 0.3877 (mpp-170) cc_final: 0.2723 (tpp-160)
REVERT: E  664 LEU cc_start: 0.6874 (tp) cc_final: 0.6030 (pp)
REVERT: E  674 ILE cc_start: 0.7420 (mm) cc_final: 0.6575 (tp)
REVERT: E  729 GLN cc_start: 0.4450 (mp10) cc_final: 0.2507 (tp-100)
REVERT: E  732 LYS cc_start: 0.6883 (tptp) cc_final: 0.6452 (mptt)
REVERT: E  766 LEU cc_start: 0.5415 (tp) cc_final: 0.5054 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1775
  time to fit residues: 18.8775
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  : 0.361 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0970
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0570
   overall best weight:    0.6256

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.137314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.125195 restraints weight = 16074.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.127012 restraints weight = 11590.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.128398 restraints weight = 8678.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5608
moved from start:          0.8957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3378  Z= 0.192
  Angle     :  0.741  10.324   4580  Z= 0.350
  Chirality :  0.046   0.172    549
  Planarity :  0.005   0.040    578
  Dihedral  :  5.194  21.375    439
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 20.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.40), residues: 405
  helix: -2.57 (0.42), residues: 117
  sheet: -1.99 (0.70), residues: 48
  loop : -1.62 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP E 411 
 HIS   0.006   0.001   HIS E 522 
 PHE   0.014   0.002   PHE E 682 
 TYR   0.017   0.002   TYR E 668 
 ARG   0.008   0.001   ARG E 688 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1901.62 seconds
wall clock time: 34 minutes 36.73 seconds (2076.73 seconds total)