Starting phenix.real_space_refine
on Wed Mar  5 19:31:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8drq_27681/03_2025/8drq_27681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8drq_27681/03_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_27681/03_2025/8drq_27681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8drq_27681/03_2025/8drq_27681.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8drq_27681/03_2025/8drq_27681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8drq_27681/03_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-5624/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: 3.89, per 1000 atoms: 1.17
  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: 0.75
  Conformation dependent library (CDL) restraints added in 360.1 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: 0.37
  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: 0.78

  Time building geometry restraints manager: 0.92 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:             4.200
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.790
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.150
-------------------------------------------------------------------------------
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  : 0.388 
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  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: 0.2418
  time to fit residues: 38.9519
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  : 0.370 
-------------------------------------------------------------------------------
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 = 47)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.126820 restraints weight = 16265.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.128614 restraints weight = 11882.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.130026 restraints weight = 9075.338|
|-----------------------------------------------------------------------------|
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  : 0.422 
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: 0.5215 (mt-10)
REVERT: E  521 LEU cc_start: 0.8209 (tt) cc_final: 0.7867 (mt)
REVERT: E  555 LEU cc_start: 0.6677 (tp) cc_final: 0.6446 (tp)
REVERT: E  592 ASN cc_start: 0.8020 (m-40) cc_final: 0.7790 (m110)
REVERT: E  603 LEU cc_start: 0.7728 (mt) cc_final: 0.7320 (mt)
REVERT: E  640 ARG cc_start: 0.4833 (mpp-170) cc_final: 0.3674 (mmp-170)
REVERT: E  737 HIS cc_start: 0.7145 (m90) cc_final: 0.6934 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2172
  time to fit residues: 28.5182
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  : 0.397 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.4461 r_free = 0.4461 target = 0.135208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.121229 restraints weight = 14274.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.123693 restraints weight = 9744.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.125609 restraints weight = 7078.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5749
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3378  Z= 0.237
  Angle     :  0.752   7.029   4580  Z= 0.360
  Chirality :  0.047   0.162    549
  Planarity :  0.005   0.056    578
  Dihedral  :  5.605  17.208    439
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 21.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.40 (0.39), residues: 405
  helix: -2.81 (0.39), residues: 122
  sheet: -1.71 (0.82), residues: 50
  loop : -2.08 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP E 647 
 HIS   0.010   0.002   HIS E 522 
 PHE   0.011   0.002   PHE E 490 
 TYR   0.023   0.003   TYR E 477 
 ARG   0.005   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
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  473 GLU cc_start: 0.5417 (tp30) cc_final: 0.5090 (tp30)
REVERT: E  592 ASN cc_start: 0.8161 (m-40) cc_final: 0.7953 (m110)
REVERT: E  597 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6729 (mm-30)
REVERT: E  640 ARG cc_start: 0.4720 (mpp-170) cc_final: 0.3504 (mmp-170)
REVERT: E  732 LYS cc_start: 0.6406 (tptp) cc_final: 0.5986 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1878
  time to fit residues: 20.8236
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  : 0.385 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
E 554 ASN
E 694 HIS
E 755 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.137865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.124297 restraints weight = 15561.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.126482 restraints weight = 11038.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.128207 restraints weight = 8210.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5705
moved from start:          0.6523

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= 0.182
  Angle     :  0.670   6.991   4580  Z= 0.322
  Chirality :  0.045   0.177    549
  Planarity :  0.005   0.048    578
  Dihedral  :  5.303  16.915    439
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.44 %
    Favored  : 96.30 %
  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 (0.40), residues: 405
  helix: -2.64 (0.42), residues: 122
  sheet: -1.83 (0.74), residues: 55
  loop : -2.04 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP E 647 
 HIS   0.006   0.001   HIS E 522 
 PHE   0.013   0.001   PHE E 490 
 TYR   0.011   0.002   TYR E 653 
 ARG   0.004   0.001   ARG E 762 

*********************** 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
  87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.340 
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  423 ASN cc_start: 0.6868 (p0) cc_final: 0.6496 (p0)
REVERT: E  521 LEU cc_start: 0.8181 (tt) cc_final: 0.7853 (mt)
REVERT: E  592 ASN cc_start: 0.8159 (m-40) cc_final: 0.7915 (m110)
REVERT: E  640 ARG cc_start: 0.4528 (mpp-170) cc_final: 0.3401 (mmp-170)
REVERT: E  664 LEU cc_start: 0.7540 (tt) cc_final: 0.6647 (pp)
REVERT: E  732 LYS cc_start: 0.6668 (tptp) cc_final: 0.6124 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1930
  time to fit residues: 19.7016
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  : 0.393 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 22 optimal weight:    0.4980
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4501 r_free = 0.4501 target = 0.137597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.123191 restraints weight = 14958.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.125450 restraints weight = 10476.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.127481 restraints weight = 7778.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5756
moved from start:          0.7005

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     :  0.669   9.918   4580  Z= 0.318
  Chirality :  0.045   0.146    549
  Planarity :  0.005   0.045    578
  Dihedral  :  5.093  17.645    439
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  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 (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: -3.24 (0.39), residues: 405
  helix: -2.54 (0.43), residues: 123
  sheet: -1.87 (0.70), residues: 55
  loop : -1.98 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP E 647 
 HIS   0.007   0.001   HIS E 522 
 PHE   0.015   0.002   PHE E 443 
 TYR   0.006   0.001   TYR E 513 
 ARG   0.004   0.000   ARG E 671 

*********************** 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
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.356 
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: 0.7702 (m-80) cc_final: 0.7074 (m-10)
REVERT: E  521 LEU cc_start: 0.8439 (tt) cc_final: 0.8116 (mt)
REVERT: E  592 ASN cc_start: 0.8040 (m-40) cc_final: 0.7831 (m110)
REVERT: E  664 LEU cc_start: 0.7407 (tt) cc_final: 0.6646 (pp)
REVERT: E  732 LYS cc_start: 0.6559 (tptp) cc_final: 0.6217 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1730
  time to fit residues: 18.1798
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  : 0.387 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.136710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.125511 restraints weight = 17569.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.127309 restraints weight = 12693.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.128769 restraints weight = 9611.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5772
moved from start:          0.7558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3378  Z= 0.237
  Angle     :  0.729   8.411   4580  Z= 0.351
  Chirality :  0.047   0.159    549
  Planarity :  0.005   0.046    578
  Dihedral  :  5.366  17.976    439
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 18.35
  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 (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: -3.45 (0.39), residues: 405
  helix: -2.72 (0.41), residues: 129
  sheet: -2.04 (0.67), residues: 55
  loop : -2.06 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP E 647 
 HIS   0.004   0.001   HIS E 694 
 PHE   0.010   0.002   PHE E 490 
 TYR   0.008   0.002   TYR E 683 
 ARG   0.006   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
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  521 LEU cc_start: 0.8342 (tt) cc_final: 0.8081 (mt)
REVERT: E  532 ASN cc_start: 0.4764 (m-40) cc_final: 0.4283 (m-40)
REVERT: E  555 LEU cc_start: 0.6798 (tp) cc_final: 0.6567 (tp)
REVERT: E  640 ARG cc_start: 0.4429 (mpp-170) cc_final: 0.3076 (mmp-170)
REVERT: E  685 ARG cc_start: 0.5905 (tpp-160) cc_final: 0.5001 (tpt170)
REVERT: E  729 GLN cc_start: 0.4210 (mp10) cc_final: 0.2417 (tt0)
REVERT: E  732 LYS cc_start: 0.6547 (tptp) cc_final: 0.6314 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1746
  time to fit residues: 17.3200
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  : 0.376 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0970
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.135547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.122122 restraints weight = 16631.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.123904 restraints weight = 12277.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.125216 restraints weight = 9468.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5752
moved from start:          0.7805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3378  Z= 0.187
  Angle     :  0.680   7.337   4580  Z= 0.327
  Chirality :  0.046   0.179    549
  Planarity :  0.004   0.046    578
  Dihedral  :  5.021  16.372    439
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.56 (0.42), residues: 124
  sheet: -2.13 (0.65), residues: 55
  loop : -1.98 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP E 411 
 HIS   0.004   0.001   HIS E 522 
 PHE   0.012   0.002   PHE E 443 
 TYR   0.007   0.001   TYR E 668 
 ARG   0.006   0.001   ARG E 666 

*********************** 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  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  521 LEU cc_start: 0.8330 (tt) cc_final: 0.8046 (mt)
REVERT: E  532 ASN cc_start: 0.4896 (m-40) cc_final: 0.4427 (m-40)
REVERT: E  555 LEU cc_start: 0.6746 (tp) cc_final: 0.6511 (tp)
REVERT: E  640 ARG cc_start: 0.4593 (mpp-170) cc_final: 0.3348 (tpp-160)
REVERT: E  685 ARG cc_start: 0.6019 (tpp-160) cc_final: 0.5443 (tpt170)
REVERT: E  729 GLN cc_start: 0.4529 (mp10) cc_final: 0.3022 (tt0)
REVERT: E  732 LYS cc_start: 0.6897 (tptp) cc_final: 0.6602 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2069
  time to fit residues: 19.9470
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  : 0.406 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 576 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.128741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.116643 restraints weight = 16703.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.118104 restraints weight = 12707.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.119362 restraints weight = 10214.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6071
moved from start:          0.9074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3378  Z= 0.365
  Angle     :  0.987  11.729   4580  Z= 0.474
  Chirality :  0.054   0.210    549
  Planarity :  0.007   0.046    578
  Dihedral  :  6.683  23.943    439
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 29.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.36 %
    Favored  : 88.64 %
  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: -3.80 (0.38), residues: 405
  helix: -3.04 (0.42), residues: 116
  sheet: -2.59 (0.64), residues: 43
  loop : -2.30 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.006   TRP E 647 
 HIS   0.010   0.002   HIS E 614 
 PHE   0.012   0.002   PHE E 490 
 TYR   0.018   0.003   TYR E 668 
 ARG   0.008   0.001   ARG E 804 

*********************** 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
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  426 ASP cc_start: 0.8574 (m-30) cc_final: 0.8361 (m-30)
REVERT: E  458 ASP cc_start: 0.6358 (m-30) cc_final: 0.6126 (p0)
REVERT: E  555 LEU cc_start: 0.6717 (tp) cc_final: 0.6366 (tp)
REVERT: E  597 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7123 (mm-30)
REVERT: E  640 ARG cc_start: 0.4187 (mpp-170) cc_final: 0.3003 (mmt180)
REVERT: E  729 GLN cc_start: 0.4805 (mp10) cc_final: 0.3090 (tt0)
REVERT: E  752 GLU cc_start: 0.5556 (mt-10) cc_final: 0.5282 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1531
  time to fit residues: 14.6680
Evaluate side-chains
  55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0020
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.4437 r_free = 0.4437 target = 0.133989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.120816 restraints weight = 16407.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.122421 restraints weight = 12518.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.123770 restraints weight = 9972.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5881
moved from start:          0.9054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3378  Z= 0.203
  Angle     :  0.778   9.951   4580  Z= 0.374
  Chirality :  0.049   0.181    549
  Planarity :  0.005   0.042    578
  Dihedral  :  5.595  19.746    439
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 19.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  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 (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: -3.65 (0.38), residues: 405
  helix: -3.00 (0.39), residues: 124
  sheet: -2.11 (0.66), residues: 49
  loop : -2.18 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.005   TRP E 411 
 HIS   0.005   0.001   HIS E 694 
 PHE   0.018   0.002   PHE E 433 
 TYR   0.012   0.002   TYR E 683 
 ARG   0.004   0.001   ARG E 541 

*********************** 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
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  426 ASP cc_start: 0.8349 (m-30) cc_final: 0.8142 (m-30)
REVERT: E  443 PHE cc_start: 0.7759 (m-80) cc_final: 0.7451 (m-10)
REVERT: E  532 ASN cc_start: 0.5191 (m-40) cc_final: 0.4532 (m-40)
REVERT: E  555 LEU cc_start: 0.6261 (tp) cc_final: 0.5995 (tp)
REVERT: E  729 GLN cc_start: 0.4952 (mp10) cc_final: 0.4339 (pm20)
REVERT: E  766 LEU cc_start: 0.5264 (tp) cc_final: 0.4979 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1453
  time to fit residues: 13.9768
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  : 0.385 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:   20.0000
   chunk 12 optimal weight:    0.3980
   chunk 11 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 = 0.4450 r_free = 0.4450 target = 0.133722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.120967 restraints weight = 16649.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.122553 restraints weight = 12434.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.123740 restraints weight = 9827.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5830
moved from start:          0.9288

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= 0.208
  Angle     :  0.765   7.704   4580  Z= 0.366
  Chirality :  0.049   0.225    549
  Planarity :  0.005   0.058    578
  Dihedral  :  5.475  18.718    439
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  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 (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: -3.42 (0.39), residues: 405
  helix: -2.97 (0.40), residues: 117
  sheet: -2.06 (0.70), residues: 50
  loop : -1.95 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP E 411 
 HIS   0.005   0.001   HIS E 522 
 PHE   0.010   0.002   PHE E 490 
 TYR   0.018   0.002   TYR E 689 
 ARG   0.003   0.001   ARG E 666 

********************** 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
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  426 ASP cc_start: 0.8130 (m-30) cc_final: 0.7879 (m-30)
REVERT: E  434 MET cc_start: 0.6020 (mmp) cc_final: 0.5810 (mmp)
REVERT: E  517 THR cc_start: 0.7464 (p) cc_final: 0.7179 (p)
REVERT: E  521 LEU cc_start: 0.8084 (mt) cc_final: 0.7807 (mt)
REVERT: E  532 ASN cc_start: 0.4774 (m-40) cc_final: 0.4147 (m-40)
REVERT: E  729 GLN cc_start: 0.4549 (mp10) cc_final: 0.4107 (pm20)
REVERT: E  766 LEU cc_start: 0.5416 (tp) cc_final: 0.5160 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1380
  time to fit residues: 13.2421
Evaluate side-chains
  59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    0.1980
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6162

-------------------------------------------------------------------------------
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 = 0.4494 r_free = 0.4494 target = 0.136690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.125893 restraints weight = 17981.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.127234 restraints weight = 13431.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.128385 restraints weight = 10710.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.9513

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= 0.194
  Angle     :  0.736   9.072   4580  Z= 0.353
  Chirality :  0.047   0.184    549
  Planarity :  0.005   0.055    578
  Dihedral  :  5.206  17.469    439
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  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: -3.33 (0.39), residues: 405
  helix: -2.93 (0.40), residues: 118
  sheet: -1.90 (0.71), residues: 49
  loop : -1.90 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.004   TRP E 411 
 HIS   0.006   0.001   HIS E 522 
 PHE   0.014   0.002   PHE E 635 
 TYR   0.017   0.002   TYR E 689 
 ARG   0.003   0.000   ARG E 541 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1801.40 seconds
wall clock time: 31 minutes 44.21 seconds (1904.21 seconds total)