Starting phenix.real_space_refine
on Tue Mar  3 14:16:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e2a_27830/03_2026/8e2a_27830.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     S      31      5.16       5
     C    3621      2.51       5
     N     985      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5768
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 686, 5456
          Classifications: {'peptide': 686}
          Link IDs: {'PTRANS': 40, 'TRANS': 645}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 312
          Classifications: {'RNA': 15}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 1, 'rna3p': 13}
          Chain breaks: 1
  Time building chain proxies: 1.48, per 1000 atoms: 0.26
  Number of scatterers: 5768
  At special positions: 0
  Unit cell: (70.35, 84.42, 109.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P      15     15.00
     O    1116      8.00
     N     985      7.00
     C    3621      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: 0.54
  Conformation dependent library (CDL) restraints added in 162.2 milliseconds
  

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1310

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 9 sheets defined
      32.9% alpha, 22.9% beta
      4 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 66
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.730A  pdb=" N   ALA A 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 340
      removed outlier: 3.664A  pdb=" N   GLU A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      Proline residue:  A 331  - end of helix
      removed outlier: 3.712A  pdb=" N   TYR A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 431
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 494 through 502
      removed outlier: 3.587A  pdb=" N   GLN A 498 " --> pdb=" O   TYR A 494 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 499 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET A 500 " --> pdb=" O   HIS A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 513
    Processing helix  chain 'A' and resid 522 through 546
      removed outlier: 3.666A  pdb=" N   ALA A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A 535 " --> pdb=" O   ASN A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 601
      removed outlier: 3.671A  pdb=" N   PHE A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 629
      removed outlier: 3.775A  pdb=" N   LEU A 618 " --> pdb=" O   GLN A 614 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER A 619 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASP A 620 " --> pdb=" O   ARG A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
    Processing helix  chain 'A' and resid 651 through 666
      removed outlier: 3.800A  pdb=" N   LEU A 655 " --> pdb=" O   ASP A 651 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ALA A 656 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 687
      removed outlier: 3.519A  pdb=" N   PHE A 686 " --> pdb=" O   PRO A 683 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ARG A 687 " --> pdb=" O   ALA A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 719
      removed outlier: 3.817A  pdb=" N   VAL A 709 " --> pdb=" O   ARG A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 766
      removed outlier: 3.646A  pdb=" N   THR A 754 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 800
      No H-bonds generated for 'chain 'A' and resid 798 through 800'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72
      removed outlier: 7.335A  pdb=" N   LEU A 110 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ILE A 238 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL A 112 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75
    Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 560
      removed outlier: 3.954A  pdb=" N   GLY A 569 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   GLN A 568 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE A 302 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LEU A 316 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU A 319 " --> pdb=" O   PRO A 281 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373
      removed outlier: 4.012A  pdb=" N   ASP A 478 " --> pdb=" O   THR A 469 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383
      removed outlier: 6.157A  pdb=" N   THR A 381 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435
    Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609
    Processing sheet with id=AA8, first strand: chain 'A' and resid 791 through 796
      removed outlier: 3.636A  pdb=" N   VAL A 791 " --> pdb=" O   VAL A 786 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ALA A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ILE A 777 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASP A 783 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810

    238 hydrogen bonds defined for protein.
    663 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      12 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1662
        1.33 -     1.45: 928
        1.45 -     1.57: 3253
        1.57 -     1.69: 28
        1.69 -     1.81: 47
  Bond restraints: 5918
  Sorted by residual:
  bond pdb=" C   ARG A 616 "
       pdb=" O   ARG A 616 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.019 1.26e-02 6.30e+03 2.16e+00
  bond pdb=" C   LEU A 359 "
       pdb=" N   PRO A 360 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.40e+00
  bond pdb=" CA  GLY A 811 "
       pdb=" C   GLY A 811 "
    ideal  model  delta    sigma   weight residual
    1.514  1.530 -0.015 1.41e-02 5.03e+03 1.21e+00
  bond pdb=" CG  LEU A 423 "
       pdb=" CD1 LEU A 423 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.19e+00
  bond pdb=" C   ARG A 616 "
       pdb=" N   MET A 617 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 1.35e-02 5.49e+03 1.10e+00
  ... (remaining 5913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 7782
        1.62 -     3.24: 234
        3.24 -     4.86: 46
        4.86 -     6.48: 8
        6.48 -     8.10: 4
  Bond angle restraints: 8074
  Sorted by residual:
  angle pdb=" C   LYS A 812 "
        pdb=" N   LYS A 813 "
        pdb=" CA  LYS A 813 "
      ideal   model   delta    sigma   weight residual
     121.61  126.86   -5.25 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" N   MET A 617 "
        pdb=" CA  MET A 617 "
        pdb=" C   MET A 617 "
      ideal   model   delta    sigma   weight residual
     112.38  116.17   -3.79 1.22e+00 6.72e-01 9.65e+00
  angle pdb=" C   ARG A 616 "
        pdb=" CA  ARG A 616 "
        pdb=" CB  ARG A 616 "
      ideal   model   delta    sigma   weight residual
     110.42  115.90   -5.48 1.99e+00 2.53e-01 7.59e+00
  angle pdb=" C   THR A 615 "
        pdb=" N   ARG A 616 "
        pdb=" CA  ARG A 616 "
      ideal   model   delta    sigma   weight residual
     121.54  126.34   -4.80 1.91e+00 2.74e-01 6.31e+00
  angle pdb=" N   SER A 848 "
        pdb=" CA  SER A 848 "
        pdb=" C   SER A 848 "
      ideal   model   delta    sigma   weight residual
     111.02  114.01   -2.99 1.22e+00 6.72e-01 5.99e+00
  ... (remaining 8069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 3336
       17.71 -    35.42: 243
       35.42 -    53.13: 45
       53.13 -    70.83: 28
       70.83 -    88.54: 11
  Dihedral angle restraints: 3663
    sinusoidal: 1651
      harmonic: 2012
  Sorted by residual:
  dihedral pdb=" CA  ASP A 824 "
           pdb=" C   ASP A 824 "
           pdb=" N   MET A 825 "
           pdb=" CA  MET A 825 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.71  -21.29     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LEU A 673 "
           pdb=" C   LEU A 673 "
           pdb=" N   TYR A 674 "
           pdb=" CA  TYR A 674 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  PHE A 699 "
           pdb=" C   PHE A 699 "
           pdb=" N   THR A 700 "
           pdb=" CA  THR A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.84  -19.16     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 3660 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 764
       0.062 -    0.124: 145
       0.124 -    0.186: 13
       0.186 -    0.248: 0
       0.248 -    0.310: 1
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" CG  LEU A 618 "
            pdb=" CB  LEU A 618 "
            pdb=" CD1 LEU A 618 "
            pdb=" CD2 LEU A 618 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CA  ARG A 616 "
            pdb=" N   ARG A 616 "
            pdb=" C   ARG A 616 "
            pdb=" CB  ARG A 616 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.57e-01
  chirality pdb=" CA  HIS A 409 "
            pdb=" N   HIS A 409 "
            pdb=" C   HIS A 409 "
            pdb=" CB  HIS A 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.12e-01
  ... (remaining 920 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 610 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO A 611 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 611 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 611 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 634 "    0.013 2.00e-02 2.50e+03   1.09e-02 2.09e+00
        pdb=" CG  PHE A 634 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 634 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 634 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 634 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 634 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 634 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 648 "    0.007 2.00e-02 2.50e+03   1.07e-02 2.00e+00
        pdb=" CG  PHE A 648 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 648 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 648 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 648 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 648 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 648 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 226
        2.72 -     3.26: 5283
        3.26 -     3.81: 8564
        3.81 -     4.35: 11167
        4.35 -     4.90: 19247
  Nonbonded interactions: 44487
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 575 "
            pdb=" OE1 GLU A 583 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD1 ASP A 651 "
            pdb=" N   LYS A 652 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" ND1 HIS A 409 "
            pdb=" OG  SER A 465 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OD2 ASP A 307 "
            pdb=" NZ  LYS A 309 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OD2 ASP A 412 "
            pdb=" NH1 ARG A 483 "
     model   vdw
     2.314 3.120
  ... (remaining 44482 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.000
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.450
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
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   0.038   5918  Z= 0.185
  Angle     :  0.709   8.103   8074  Z= 0.379
  Chirality :  0.047   0.310    923
  Planarity :  0.005   0.048    990
  Dihedral  : 14.471  88.543   2353
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.31), residues: 680
  helix:  1.18 (0.36), residues: 208
  sheet:  0.34 (0.38), residues: 161
  loop : -1.32 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  74 
 TYR   0.018   0.002   TYR A 853 
 PHE   0.025   0.002   PHE A 634 
 TRP   0.016   0.002   TRP A 468 
 HIS   0.005   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 5918)
  covalent geometry    : angle       0.70874 ( 8074)
  hydrogen bonds       : bond        0.10103 (  250)
  hydrogen bonds       : angle       5.39520 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   54 MET cc_start: 0.6703 (tpt) cc_final: 0.6386 (tpp)
REVERT: A   74 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6557 (ttp-110)
REVERT: A  242 LYS cc_start: 0.7942 (mttt) cc_final: 0.7730 (mmtm)
REVERT: A  318 GLN cc_start: 0.7127 (tt0) cc_final: 0.6890 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.7658
  time to fit residues: 73.4994
Evaluate side-chains
  55 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
A 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.113191 restraints weight = 6317.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.32
r_work: 0.3262 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5918  Z= 0.125
  Angle     :  0.580   9.709   8074  Z= 0.291
  Chirality :  0.042   0.138    923
  Planarity :  0.004   0.040    990
  Dihedral  : 12.334  73.042    985
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.62 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.32), residues: 680
  helix:  1.65 (0.37), residues: 209
  sheet:  0.24 (0.38), residues: 170
  loop : -1.12 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 803 
 TYR   0.010   0.001   TYR A 674 
 PHE   0.013   0.002   PHE A 648 
 TRP   0.014   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5918)
  covalent geometry    : angle       0.58024 ( 8074)
  hydrogen bonds       : bond        0.04363 (  250)
  hydrogen bonds       : angle       4.29258 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 GLN cc_start: 0.7477 (tt0) cc_final: 0.7126 (mt0)
REVERT: A  681 GLN cc_start: 0.7424 (mm110) cc_final: 0.7175 (mm110)
REVERT: A  841 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6874 (mt-10)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.6175
  time to fit residues: 41.8992
Evaluate side-chains
  58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 8 optimal weight:    0.0370
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.9464

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.154724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.112649 restraints weight = 6283.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.31
r_work: 0.3259 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5918  Z= 0.124
  Angle     :  0.551   8.741   8074  Z= 0.274
  Chirality :  0.042   0.137    923
  Planarity :  0.004   0.040    990
  Dihedral  : 12.093  73.161    985
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.28 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.32), residues: 680
  helix:  1.94 (0.37), residues: 205
  sheet:  0.35 (0.38), residues: 170
  loop : -1.06 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 803 
 TYR   0.009   0.001   TYR A 674 
 PHE   0.012   0.001   PHE A 757 
 TRP   0.013   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5918)
  covalent geometry    : angle       0.55076 ( 8074)
  hydrogen bonds       : bond        0.04193 (  250)
  hydrogen bonds       : angle       4.07127 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 GLN cc_start: 0.7455 (tt0) cc_final: 0.7100 (mt0)
REVERT: A  523 GLU cc_start: 0.7403 (mp0) cc_final: 0.6607 (mm-30)
REVERT: A  841 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6875 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.7120
  time to fit residues: 42.9342
Evaluate side-chains
  58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.155009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112159 restraints weight = 6248.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.37
r_work: 0.3226 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5918  Z= 0.112
  Angle     :  0.523   7.736   8074  Z= 0.262
  Chirality :  0.041   0.136    923
  Planarity :  0.004   0.038    990
  Dihedral  : 11.947  73.167    985
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.28 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.32), residues: 680
  helix:  2.11 (0.37), residues: 205
  sheet:  0.34 (0.38), residues: 170
  loop : -0.97 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 803 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.011   0.001   PHE A 757 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5918)
  covalent geometry    : angle       0.52301 ( 8074)
  hydrogen bonds       : bond        0.03959 (  250)
  hydrogen bonds       : angle       3.92837 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.6896 (tpt) cc_final: 0.6499 (tpt)
REVERT: A  318 GLN cc_start: 0.7394 (tt0) cc_final: 0.7051 (mt0)
REVERT: A  523 GLU cc_start: 0.7357 (mp0) cc_final: 0.6531 (mm-30)
REVERT: A  841 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6853 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 60
  average time/residue: 0.7060
  time to fit residues: 44.0556
Evaluate side-chains
  58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0670
   chunk 44 optimal weight:    0.4980
   chunk 31 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.156570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.113501 restraints weight = 6335.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.40
r_work: 0.3253 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5918  Z= 0.095
  Angle     :  0.489   7.160   8074  Z= 0.248
  Chirality :  0.040   0.133    923
  Planarity :  0.004   0.034    990
  Dihedral  : 11.802  73.160    985
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.77 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.32), residues: 680
  helix:  2.35 (0.37), residues: 205
  sheet:  0.46 (0.38), residues: 168
  loop : -0.85 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 803 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.010   0.001   PHE A 757 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.002   0.000   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 5918)
  covalent geometry    : angle       0.48914 ( 8074)
  hydrogen bonds       : bond        0.03540 (  250)
  hydrogen bonds       : angle       3.76293 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  318 GLN cc_start: 0.7372 (tt0) cc_final: 0.7037 (mt0)
REVERT: A  523 GLU cc_start: 0.7331 (mp0) cc_final: 0.6483 (mm-30)
REVERT: A  841 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6863 (mt-10)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.6233
  time to fit residues: 42.3493
Evaluate side-chains
  56 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0270
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 663 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.157283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114224 restraints weight = 6307.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.40
r_work: 0.3257 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5918  Z= 0.092
  Angle     :  0.490   9.579   8074  Z= 0.243
  Chirality :  0.040   0.133    923
  Planarity :  0.004   0.031    990
  Dihedral  : 11.729  73.156    985
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.94 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.33), residues: 680
  helix:  2.33 (0.37), residues: 211
  sheet:  0.43 (0.39), residues: 170
  loop : -0.80 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 803 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.009   0.001   PHE A 757 
 TRP   0.011   0.001   TRP A 468 
 HIS   0.001   0.000   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 5918)
  covalent geometry    : angle       0.48998 ( 8074)
  hydrogen bonds       : bond        0.03476 (  250)
  hydrogen bonds       : angle       3.72118 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.7040 (mmm) cc_final: 0.6606 (tpt)
REVERT: A  318 GLN cc_start: 0.7371 (tt0) cc_final: 0.7020 (mt0)
REVERT: A  523 GLU cc_start: 0.7339 (mp0) cc_final: 0.6487 (mm-30)
REVERT: A  681 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7569 (mm110)
REVERT: A  841 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6856 (mt-10)
  outliers start: 8
  outliers final: 6
  residues processed: 61
  average time/residue: 0.7036
  time to fit residues: 44.6859
Evaluate side-chains
  60 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0470
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.154455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111125 restraints weight = 6316.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.40
r_work: 0.3214 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5918  Z= 0.133
  Angle     :  0.552   9.770   8074  Z= 0.275
  Chirality :  0.041   0.139    923
  Planarity :  0.004   0.036    990
  Dihedral  : 11.738  73.122    985
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.10 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.33), residues: 680
  helix:  2.16 (0.37), residues: 211
  sheet:  0.42 (0.39), residues: 170
  loop : -0.86 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 803 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.013   0.002   PHE A 757 
 TRP   0.011   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 5918)
  covalent geometry    : angle       0.55226 ( 8074)
  hydrogen bonds       : bond        0.04086 (  250)
  hydrogen bonds       : angle       3.87234 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.7023 (mmm) cc_final: 0.6624 (tpt)
REVERT: A  318 GLN cc_start: 0.7440 (tt0) cc_final: 0.7078 (mt0)
REVERT: A  523 GLU cc_start: 0.7383 (mp0) cc_final: 0.6591 (mm-30)
REVERT: A  681 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7613 (mm110)
REVERT: A  841 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6867 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 58
  average time/residue: 0.7144
  time to fit residues: 42.9898
Evaluate side-chains
  57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.156455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113211 restraints weight = 6263.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.38
r_work: 0.3248 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5918  Z= 0.102
  Angle     :  0.512  10.008   8074  Z= 0.257
  Chirality :  0.040   0.135    923
  Planarity :  0.004   0.032    990
  Dihedral  : 11.694  73.144    985
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.43 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.33), residues: 680
  helix:  2.07 (0.37), residues: 217
  sheet:  0.46 (0.39), residues: 170
  loop : -0.86 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 803 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.013   0.001   PHE A  80 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.002   0.000   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5918)
  covalent geometry    : angle       0.51212 ( 8074)
  hydrogen bonds       : bond        0.03622 (  250)
  hydrogen bonds       : angle       3.75068 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   54 MET cc_start: 0.6982 (mmm) cc_final: 0.6603 (tpt)
REVERT: A  523 GLU cc_start: 0.7345 (mp0) cc_final: 0.6540 (mm-30)
REVERT: A  681 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7675 (mm110)
REVERT: A  841 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6868 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.6351
  time to fit residues: 37.6161
Evaluate side-chains
  54 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 614 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112247 restraints weight = 6279.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.40
r_work: 0.3229 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5918  Z= 0.112
  Angle     :  0.527  11.021   8074  Z= 0.263
  Chirality :  0.041   0.136    923
  Planarity :  0.004   0.035    990
  Dihedral  : 11.682  73.133    985
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.60 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.33), residues: 680
  helix:  2.04 (0.37), residues: 217
  sheet:  0.45 (0.39), residues: 170
  loop : -0.89 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 483 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.020   0.001   PHE A  80 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5918)
  covalent geometry    : angle       0.52705 ( 8074)
  hydrogen bonds       : bond        0.03814 (  250)
  hydrogen bonds       : angle       3.80677 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   54 MET cc_start: 0.7002 (mmm) cc_final: 0.6413 (tpt)
REVERT: A  523 GLU cc_start: 0.7347 (mp0) cc_final: 0.6551 (mm-30)
REVERT: A  681 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7663 (mm110)
REVERT: A  841 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6865 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 53
  average time/residue: 0.6565
  time to fit residues: 36.2008
Evaluate side-chains
  53 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 68 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.150431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.107998 restraints weight = 6360.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.34
r_work: 0.3172 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5918  Z= 0.193
  Angle     :  0.628  11.653   8074  Z= 0.309
  Chirality :  0.044   0.145    923
  Planarity :  0.005   0.046    990
  Dihedral  : 11.808  73.175    985
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.43 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.32), residues: 680
  helix:  1.63 (0.36), residues: 217
  sheet:  0.37 (0.39), residues: 170
  loop : -1.05 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 543 
 TYR   0.010   0.001   TYR A 575 
 PHE   0.025   0.002   PHE A  80 
 TRP   0.010   0.002   TRP A 468 
 HIS   0.005   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 5918)
  covalent geometry    : angle       0.62782 ( 8074)
  hydrogen bonds       : bond        0.05038 (  250)
  hydrogen bonds       : angle       4.14251 (  687)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   54 MET cc_start: 0.7056 (mmm) cc_final: 0.6395 (tpt)
REVERT: A  523 GLU cc_start: 0.7433 (mp0) cc_final: 0.6701 (mm-30)
REVERT: A  681 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7673 (mm110)
REVERT: A  841 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6876 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 55
  average time/residue: 0.6995
  time to fit residues: 40.0996
Evaluate side-chains
  53 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  835 THR
Chi-restraints excluded: chain A residue  841 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.154148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.112041 restraints weight = 6219.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.27
r_work: 0.3263 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5918  Z= 0.118
  Angle     :  0.548  11.776   8074  Z= 0.272
  Chirality :  0.041   0.138    923
  Planarity :  0.004   0.040    990
  Dihedral  : 11.734  73.126    985
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.93 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.33), residues: 680
  helix:  1.86 (0.37), residues: 217
  sheet:  0.46 (0.39), residues: 168
  loop : -0.98 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 483 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.022   0.001   PHE A  80 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5918)
  covalent geometry    : angle       0.54834 ( 8074)
  hydrogen bonds       : bond        0.04078 (  250)
  hydrogen bonds       : angle       3.94957 (  687)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2665.84 seconds
wall clock time: 46 minutes 0.86 seconds (2760.86 seconds total)