Starting phenix.real_space_refine
on Fri Aug 22 17:59:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ugc_64136/08_2025/9ugc_64136.map"
  }
  resolution = 3.52
  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=   0.005 sd=   0.055
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      32      5.16       5
     C    4252      2.51       5
     N    1096      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6606
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 846, 6494
          Classifications: {'peptide': 846}
          Link IDs: {'PTRANS': 33, 'TRANS': 812}
    Chain: "B"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 112
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 1.68, per 1000 atoms: 0.25
  Number of scatterers: 6606
  At special positions: 0
  Unit cell: (94.668, 83.349, 128.625, 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      32     16.00
     O    1226      8.00
     N    1096      7.00
     C    4252      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: 0.60
  Conformation dependent library (CDL) restraints added in 369.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      61.0% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.777A  pdb=" N   LEU A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 100
    Processing helix  chain 'A' and resid 110 through 121
      removed outlier: 3.865A  pdb=" N   LYS A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 138
    Processing helix  chain 'A' and resid 140 through 173
    Processing helix  chain 'A' and resid 192 through 196
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 284 through 315
    Processing helix  chain 'A' and resid 318 through 334
      removed outlier: 3.975A  pdb=" N   ILE A 332 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A 334 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 356
    Processing helix  chain 'A' and resid 363 through 371
      removed outlier: 3.944A  pdb=" N   GLU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 420 through 430
    Processing helix  chain 'A' and resid 433 through 441
      removed outlier: 4.306A  pdb=" N   THR A 441 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 488
      removed outlier: 3.705A  pdb=" N   ASP A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 509
    Processing helix  chain 'A' and resid 540 through 550
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.797A  pdb=" N   GLU A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 585
    Processing helix  chain 'A' and resid 593 through 604
    Processing helix  chain 'A' and resid 611 through 625
      removed outlier: 3.614A  pdb=" N   TYR A 616 " --> pdb=" O   PRO A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 637
      No H-bonds generated for 'chain 'A' and resid 635 through 637'
    Processing helix  chain 'A' and resid 638 through 645
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 670 through 713
      removed outlier: 3.649A  pdb=" N   ILE A 674 " --> pdb=" O   GLY A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
      removed outlier: 3.677A  pdb=" N   ALA A 732 " --> pdb=" O   PHE A 728 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   THR A 733 " --> pdb=" O   ALA A 729 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 734 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A 735 " --> pdb=" O   VAL A 731 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA A 737 " --> pdb=" O   THR A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 779
      removed outlier: 3.767A  pdb=" N   LEU A 779 " --> pdb=" O   THR A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 805
    Processing helix  chain 'A' and resid 805 through 811
      removed outlier: 3.613A  pdb=" N   ILE A 809 " --> pdb=" O   TRP A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 843
    Processing helix  chain 'A' and resid 851 through 878
      removed outlier: 3.637A  pdb=" N   THR A 878 " --> pdb=" O   TYR A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 888
      removed outlier: 3.623A  pdb=" N   ASP A 883 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 918
      removed outlier: 4.059A  pdb=" N   THR A 918 " --> pdb=" O   HIS A 914 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
    Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184
    Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 204
      removed outlier: 7.157A  pdb=" N   ASP A 213 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239
    Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 360
      removed outlier: 6.392A  pdb=" N   ALA A 650 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE A 649 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   MET A 631 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 630 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   THR A 632 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   CYS A 376 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   PHE A 607 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   MET A 556 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390
      removed outlier: 7.574A  pdb=" N   TRP A 524 " --> pdb=" O   ARG A 519 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ARG A 519 " --> pdb=" O   TRP A 524 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   ILE A 526 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG A 517 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 528 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   LYS A 457 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   THR A 459 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE A 448 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1224 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: 1.19

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2141
        1.35 -     1.46: 1504
        1.46 -     1.58: 3039
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 6739
  Sorted by residual:
  bond pdb=" N   LEU A  88 "
       pdb=" CA  LEU A  88 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 1.22e-02 6.72e+03 5.90e+00
  bond pdb=" N   LEU A 300 "
       pdb=" CA  LEU A 300 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.96e+00
  bond pdb=" CB  ARG A  97 "
       pdb=" CG  ARG A  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.37e+00
  bond pdb=" N   ASN A 178 "
       pdb=" CA  ASN A 178 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.29e-02 6.01e+03 2.17e+00
  bond pdb=" CB  VAL A 723 "
       pdb=" CG2 VAL A 723 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  ... (remaining 6734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 9054
        2.54 -     5.08: 81
        5.08 -     7.62: 12
        7.62 -    10.17: 3
       10.17 -    12.71: 1
  Bond angle restraints: 9151
  Sorted by residual:
  angle pdb=" CB  ARG A  97 "
        pdb=" CG  ARG A  97 "
        pdb=" CD  ARG A  97 "
      ideal   model   delta    sigma   weight residual
     111.30  124.01  -12.71 2.30e+00 1.89e-01 3.05e+01
  angle pdb=" CA  ARG A  97 "
        pdb=" CB  ARG A  97 "
        pdb=" CG  ARG A  97 "
      ideal   model   delta    sigma   weight residual
     114.10  124.13  -10.03 2.00e+00 2.50e-01 2.51e+01
  angle pdb=" CB  MET A 105 "
        pdb=" CG  MET A 105 "
        pdb=" SD  MET A 105 "
      ideal   model   delta    sigma   weight residual
     112.70  122.76  -10.06 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C   ASN A 178 "
        pdb=" CA  ASN A 178 "
        pdb=" CB  ASN A 178 "
      ideal   model   delta    sigma   weight residual
     110.42  115.96   -5.54 1.99e+00 2.53e-01 7.75e+00
  angle pdb=" CA  LEU A 223 "
        pdb=" CB  LEU A 223 "
        pdb=" CG  LEU A 223 "
      ideal   model   delta    sigma   weight residual
     116.30  126.04   -9.74 3.50e+00 8.16e-02 7.74e+00
  ... (remaining 9146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3475
       17.95 -    35.89: 412
       35.89 -    53.84: 85
       53.84 -    71.78: 18
       71.78 -    89.73: 11
  Dihedral angle restraints: 4001
    sinusoidal: 1548
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" CA  THR A 245 "
           pdb=" C   THR A 245 "
           pdb=" N   PHE A 246 "
           pdb=" CA  PHE A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.67  -19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ASP B  41 "
           pdb=" CB  ASP B  41 "
           pdb=" CG  ASP B  41 "
           pdb=" OD1 ASP B  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.96   56.96     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CB  GLU A 901 "
           pdb=" CG  GLU A 901 "
           pdb=" CD  GLU A 901 "
           pdb=" OE1 GLU A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.42   88.42     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 729
       0.039 -    0.077: 259
       0.077 -    0.116: 65
       0.116 -    0.155: 12
       0.155 -    0.193: 3
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CA  LEU A 300 "
            pdb=" N   LEU A 300 "
            pdb=" C   LEU A 300 "
            pdb=" CB  LEU A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.35e-01
  chirality pdb=" CG  LEU A 427 "
            pdb=" CB  LEU A 427 "
            pdb=" CD1 LEU A 427 "
            pdb=" CD2 LEU A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" CB  VAL A 197 "
            pdb=" CA  VAL A 197 "
            pdb=" CG1 VAL A 197 "
            pdb=" CG2 VAL A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1065 not shown)

  Planarity restraints: 1160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  87 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.22e+00
        pdb=" C   GLY A  87 "    0.040 2.00e-02 2.50e+03
        pdb=" O   GLY A  87 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  88 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  73 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO A  74 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 126 "   -0.014 2.00e-02 2.50e+03   1.37e-02 3.27e+00
        pdb=" CG  PHE A 126 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 126 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 126 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 126 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 126 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 126 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1157 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 520
        2.74 -     3.28: 7075
        3.28 -     3.82: 11439
        3.82 -     4.36: 13077
        4.36 -     4.90: 22410
  Nonbonded interactions: 54521
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 296 "
            pdb=" CD1 LEU A 300 "
     model   vdw
     2.197 3.460
  nonbonded pdb=" NE1 TRP A 805 "
            pdb=" OD2 ASP A 833 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   ILE A 366 "
            pdb=" OG  SER A 681 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" ND1 HIS A 285 "
            pdb=" OE2 GLU A 367 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   SER A 770 "
            pdb=" OG1 THR A 773 "
     model   vdw
     2.316 3.040
  ... (remaining 54516 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.880
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6739  Z= 0.143
  Angle     :  0.633  12.706   9151  Z= 0.323
  Chirality :  0.042   0.193   1068
  Planarity :  0.004   0.053   1160
  Dihedral  : 16.673  89.729   2427
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 25.11 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.30), residues: 856
  helix:  1.64 (0.24), residues: 481
  sheet: -0.67 (0.53), residues: 80
  loop : -0.21 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  97 
 TYR   0.016   0.001   TYR A 874 
 PHE   0.032   0.002   PHE A 126 
 TRP   0.028   0.002   TRP A 524 
 HIS   0.002   0.000   HIS A 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6739)
  covalent geometry    : angle       0.63292 ( 9151)
  hydrogen bonds       : bond        0.12364 (  418)
  hydrogen bonds       : angle       5.37668 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 112
  average time/residue: 0.0617
  time to fit residues: 10.1901
Evaluate side-chains
  105 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.168723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.132225 restraints weight = 9729.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132169 restraints weight = 8328.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.134379 restraints weight = 6975.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.134323 restraints weight = 5208.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.134746 restraints weight = 4423.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6739  Z= 0.135
  Angle     :  0.537   6.466   9151  Z= 0.276
  Chirality :  0.041   0.152   1068
  Planarity :  0.004   0.047   1160
  Dihedral  :  4.204  40.968    914
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.12 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.29), residues: 856
  helix:  1.73 (0.23), residues: 491
  sheet: -0.68 (0.49), residues: 97
  loop : -0.58 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.015   0.001   TYR A 691 
 PHE   0.032   0.001   PHE A 126 
 TRP   0.017   0.001   TRP A 524 
 HIS   0.002   0.001   HIS A 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6739)
  covalent geometry    : angle       0.53745 ( 9151)
  hydrogen bonds       : bond        0.03646 (  418)
  hydrogen bonds       : angle       4.50208 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7397 (tptt) cc_final: 0.7099 (tptt)
REVERT: A  443 TYR cc_start: 0.7130 (m-80) cc_final: 0.6730 (m-10)
REVERT: A  542 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7500 (tp-100)
REVERT: A  609 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7869 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 125
  average time/residue: 0.0615
  time to fit residues: 11.4070
Evaluate side-chains
  117 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 GLN
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.164728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126631 restraints weight = 9706.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.126339 restraints weight = 9789.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.128215 restraints weight = 8158.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.128433 restraints weight = 5716.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129447 restraints weight = 5048.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6739  Z= 0.207
  Angle     :  0.606   7.473   9151  Z= 0.309
  Chirality :  0.043   0.138   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  4.079  16.280    912
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.98 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.29), residues: 856
  helix:  1.53 (0.23), residues: 491
  sheet: -0.82 (0.48), residues: 96
  loop : -0.58 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  97 
 TYR   0.017   0.002   TYR A 694 
 PHE   0.023   0.002   PHE A 246 
 TRP   0.013   0.001   TRP A 524 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 6739)
  covalent geometry    : angle       0.60569 ( 9151)
  hydrogen bonds       : bond        0.03800 (  418)
  hydrogen bonds       : angle       4.51870 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7423 (tptt) cc_final: 0.7185 (tptt)
REVERT: A  346 MET cc_start: 0.8482 (mmp) cc_final: 0.7998 (mmp)
REVERT: A  542 GLN cc_start: 0.7704 (tp40) cc_final: 0.7469 (tp-100)
REVERT: B   49 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5981 (tp30)
  outliers start: 30
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0688
  time to fit residues: 12.8650
Evaluate side-chains
  130 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain B residue   49 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:    0.0170
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.168072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.131213 restraints weight = 9687.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.131314 restraints weight = 7876.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.133423 restraints weight = 6673.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133414 restraints weight = 4986.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133725 restraints weight = 4298.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6739  Z= 0.125
  Angle     :  0.553   8.491   9151  Z= 0.276
  Chirality :  0.041   0.139   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  3.948  16.370    912
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 23.97 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.29), residues: 856
  helix:  1.70 (0.23), residues: 489
  sheet: -0.84 (0.47), residues: 97
  loop : -0.66 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.015   0.001   TYR A 691 
 PHE   0.032   0.002   PHE A 126 
 TRP   0.015   0.001   TRP A 524 
 HIS   0.002   0.000   HIS A 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6739)
  covalent geometry    : angle       0.55327 ( 9151)
  hydrogen bonds       : bond        0.03310 (  418)
  hydrogen bonds       : angle       4.33345 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7809 (tt) cc_final: 0.7450 (tt)
REVERT: A  109 LYS cc_start: 0.7415 (tptt) cc_final: 0.7124 (tptt)
REVERT: A  542 GLN cc_start: 0.7615 (tp40) cc_final: 0.7368 (tp-100)
REVERT: A  609 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7789 (tm-30)
REVERT: A  844 TRP cc_start: 0.7457 (m-10) cc_final: 0.5495 (m100)
  outliers start: 31
  outliers final: 22
  residues processed: 131
  average time/residue: 0.0627
  time to fit residues: 12.2176
Evaluate side-chains
  124 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.165363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127739 restraints weight = 9914.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.127675 restraints weight = 9784.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129358 restraints weight = 8012.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.129677 restraints weight = 5778.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.130474 restraints weight = 4981.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6739  Z= 0.165
  Angle     :  0.586   7.607   9151  Z= 0.294
  Chirality :  0.042   0.142   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.994  15.780    912
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 24.40 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 856
  helix:  1.74 (0.23), residues: 489
  sheet: -0.65 (0.48), residues: 96
  loop : -0.67 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 884 
 TYR   0.016   0.001   TYR A 691 
 PHE   0.022   0.002   PHE A 246 
 TRP   0.015   0.001   TRP A 524 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6739)
  covalent geometry    : angle       0.58600 ( 9151)
  hydrogen bonds       : bond        0.03419 (  418)
  hydrogen bonds       : angle       4.39202 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 LEU cc_start: 0.7584 (tt) cc_final: 0.7174 (tt)
REVERT: A  109 LYS cc_start: 0.7420 (tptt) cc_final: 0.7119 (tptt)
REVERT: A  346 MET cc_start: 0.8445 (mmp) cc_final: 0.8141 (mmp)
REVERT: A  542 GLN cc_start: 0.7609 (tp40) cc_final: 0.7366 (tp-100)
REVERT: A  844 TRP cc_start: 0.7426 (m-10) cc_final: 0.5504 (m100)
  outliers start: 33
  outliers final: 29
  residues processed: 134
  average time/residue: 0.0644
  time to fit residues: 12.6829
Evaluate side-chains
  128 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 41 optimal weight:    0.0570
   chunk 7 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.167935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.130936 restraints weight = 9814.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.130918 restraints weight = 8301.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.133232 restraints weight = 6910.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.133071 restraints weight = 4998.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133357 restraints weight = 4422.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6739  Z= 0.134
  Angle     :  0.581   8.417   9151  Z= 0.289
  Chirality :  0.042   0.157   1068
  Planarity :  0.004   0.044   1160
  Dihedral  :  3.933  17.635    912
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.39 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.29), residues: 856
  helix:  1.76 (0.23), residues: 489
  sheet: -0.54 (0.50), residues: 96
  loop : -0.71 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 884 
 TYR   0.016   0.001   TYR A 691 
 PHE   0.031   0.001   PHE A 126 
 TRP   0.012   0.001   TRP A 817 
 HIS   0.002   0.000   HIS A 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6739)
  covalent geometry    : angle       0.58127 ( 9151)
  hydrogen bonds       : bond        0.03344 (  418)
  hydrogen bonds       : angle       4.34107 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 111
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 LEU cc_start: 0.7807 (tt) cc_final: 0.7402 (tt)
REVERT: A  109 LYS cc_start: 0.7411 (tptt) cc_final: 0.7077 (tptt)
REVERT: A  346 MET cc_start: 0.8414 (mmp) cc_final: 0.8076 (mmp)
REVERT: A  844 TRP cc_start: 0.7449 (m-10) cc_final: 0.5554 (m100)
  outliers start: 36
  outliers final: 29
  residues processed: 137
  average time/residue: 0.0634
  time to fit residues: 12.9414
Evaluate side-chains
  127 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.166160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.128770 restraints weight = 9695.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129447 restraints weight = 8237.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.131053 restraints weight = 6926.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.131128 restraints weight = 4935.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.131454 restraints weight = 4448.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6739  Z= 0.170
  Angle     :  0.616   8.614   9151  Z= 0.309
  Chirality :  0.042   0.193   1068
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.021  18.692    912
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 25.11 %
    Favored  : 70.07 %
  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 aren not related in a simple way.
  whole:  1.02 (0.29), residues: 856
  helix:  1.71 (0.23), residues: 490
  sheet: -0.73 (0.47), residues: 101
  loop : -0.65 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 682 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.013   0.001   PHE A 666 
 TRP   0.013   0.001   TRP A 817 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6739)
  covalent geometry    : angle       0.61581 ( 9151)
  hydrogen bonds       : bond        0.03442 (  418)
  hydrogen bonds       : angle       4.33509 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7547 (tptt) cc_final: 0.7141 (tptt)
REVERT: A  141 TRP cc_start: 0.7376 (m-10) cc_final: 0.6694 (m100)
REVERT: A  346 MET cc_start: 0.8447 (mmp) cc_final: 0.8142 (mmp)
REVERT: A  542 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7490 (tp-100)
REVERT: A  844 TRP cc_start: 0.7444 (m-10) cc_final: 0.5508 (m100)
  outliers start: 34
  outliers final: 32
  residues processed: 135
  average time/residue: 0.0634
  time to fit residues: 12.5178
Evaluate side-chains
  134 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.165860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128530 restraints weight = 9817.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128809 restraints weight = 8413.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.130473 restraints weight = 6828.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.130775 restraints weight = 5036.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.131008 restraints weight = 4483.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6739  Z= 0.170
  Angle     :  0.635  11.194   9151  Z= 0.315
  Chirality :  0.043   0.189   1068
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.053  17.871    912
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 24.96 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 856
  helix:  1.71 (0.23), residues: 489
  sheet: -0.68 (0.48), residues: 101
  loop : -0.58 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 884 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.035   0.002   PHE A 126 
 TRP   0.015   0.001   TRP A 817 
 HIS   0.003   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6739)
  covalent geometry    : angle       0.63463 ( 9151)
  hydrogen bonds       : bond        0.03450 (  418)
  hydrogen bonds       : angle       4.33735 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7541 (tptt) cc_final: 0.6898 (tptp)
REVERT: A  346 MET cc_start: 0.8440 (mmp) cc_final: 0.8140 (mmp)
REVERT: A  542 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7388 (tp-100)
REVERT: A  844 TRP cc_start: 0.7428 (m-10) cc_final: 0.5478 (m100)
  outliers start: 41
  outliers final: 36
  residues processed: 140
  average time/residue: 0.0633
  time to fit residues: 13.0465
Evaluate side-chains
  139 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0980
   chunk 42 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.166087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.129395 restraints weight = 9795.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.129580 restraints weight = 8701.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.132006 restraints weight = 6994.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.131609 restraints weight = 5076.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.131978 restraints weight = 4953.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6739  Z= 0.149
  Angle     :  0.628  12.130   9151  Z= 0.312
  Chirality :  0.043   0.174   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  4.029  17.185    912
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.24 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 856
  helix:  1.73 (0.23), residues: 489
  sheet: -0.67 (0.51), residues: 91
  loop : -0.53 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.016   0.001   PHE A 778 
 TRP   0.016   0.001   TRP A 817 
 HIS   0.002   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6739)
  covalent geometry    : angle       0.62789 ( 9151)
  hydrogen bonds       : bond        0.03319 (  418)
  hydrogen bonds       : angle       4.32594 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 107
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7520 (tptt) cc_final: 0.7233 (tptt)
REVERT: A  346 MET cc_start: 0.8436 (mmp) cc_final: 0.8114 (mmp)
REVERT: A  844 TRP cc_start: 0.7315 (m-10) cc_final: 0.5432 (m100)
  outliers start: 35
  outliers final: 32
  residues processed: 133
  average time/residue: 0.0643
  time to fit residues: 12.4136
Evaluate side-chains
  139 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  731 VAL
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.164212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126932 restraints weight = 9792.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127413 restraints weight = 8564.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129146 restraints weight = 7124.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129279 restraints weight = 5170.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.129750 restraints weight = 4641.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6739  Z= 0.206
  Angle     :  0.675  12.070   9151  Z= 0.335
  Chirality :  0.044   0.179   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  4.137  17.591    912
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 26.24 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.29), residues: 856
  helix:  1.65 (0.23), residues: 489
  sheet: -0.70 (0.52), residues: 91
  loop : -0.55 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 909 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.019   0.002   PHE A 778 
 TRP   0.018   0.002   TRP A 817 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 6739)
  covalent geometry    : angle       0.67538 ( 9151)
  hydrogen bonds       : bond        0.03539 (  418)
  hydrogen bonds       : angle       4.40806 ( 1224)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7447 (tptt) cc_final: 0.6915 (tptp)
REVERT: A  346 MET cc_start: 0.8457 (mmp) cc_final: 0.8189 (mmp)
REVERT: A  542 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7455 (tp-100)
REVERT: A  740 ASN cc_start: 0.7562 (t0) cc_final: 0.7305 (t0)
REVERT: A  844 TRP cc_start: 0.7415 (m-10) cc_final: 0.5512 (m100)
  outliers start: 37
  outliers final: 34
  residues processed: 137
  average time/residue: 0.0624
  time to fit residues: 12.3654
Evaluate side-chains
  140 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.166525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.129937 restraints weight = 9765.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130236 restraints weight = 8148.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132209 restraints weight = 6723.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132269 restraints weight = 4824.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.132506 restraints weight = 4386.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6739  Z= 0.144
  Angle     :  0.664  12.307   9151  Z= 0.325
  Chirality :  0.043   0.166   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  4.083  18.976    912
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.67 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 856
  helix:  1.71 (0.23), residues: 488
  sheet: -0.60 (0.52), residues: 91
  loop : -0.51 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  97 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.012   0.001   PHE A 666 
 TRP   0.017   0.001   TRP A 817 
 HIS   0.002   0.000   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6739)
  covalent geometry    : angle       0.66410 ( 9151)
  hydrogen bonds       : bond        0.03325 (  418)
  hydrogen bonds       : angle       4.33282 ( 1224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1234.69 seconds
wall clock time: 22 minutes 10.80 seconds (1330.80 seconds total)