Starting phenix.real_space_refine
on Wed Feb  4 02:13:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hmv_52298/02_2026/9hmv_52298.map"
  }
  resolution = 2.9
  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=  -0.024 sd=   0.311
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      58      5.16       5
     C    5247      2.51       5
     N    1387      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8234
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 940, 7647
          Classifications: {'peptide': 940}
          Link IDs: {'PTRANS': 18, 'TRANS': 921}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 4, 'TRANS': 68}
  Time building chain proxies: 1.82, per 1000 atoms: 0.22
  Number of scatterers: 8234
  At special positions: 0
  Unit cell: (116.41, 134.458, 118.214, 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      58     16.00
     O    1542      8.00
     N    1387      7.00
     C    5247      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: 0.61
  Conformation dependent library (CDL) restraints added in 337.5 milliseconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      80.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 94 through 109
    Processing helix  chain 'A' and resid 109 through 124
      removed outlier: 3.671A  pdb=" N   ALA A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 139
    Processing helix  chain 'A' and resid 140 through 151
    Processing helix  chain 'A' and resid 165 through 187
      removed outlier: 3.537A  pdb=" N   SER A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
    Processing helix  chain 'A' and resid 195 through 208
    Processing helix  chain 'A' and resid 212 through 255
    Processing helix  chain 'A' and resid 262 through 292
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 301 through 319
    Processing helix  chain 'A' and resid 319 through 324
    Processing helix  chain 'A' and resid 325 through 336
      removed outlier: 5.380A  pdb=" N   TYR A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL A 332 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
      removed outlier: 3.652A  pdb=" N   LEU A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 380
      removed outlier: 4.605A  pdb=" N   LEU A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   PHE A 367 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   ASP A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   ARG A 374 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 401
    Processing helix  chain 'A' and resid 406 through 415
    Processing helix  chain 'A' and resid 416 through 419
    Processing helix  chain 'A' and resid 421 through 437
    Processing helix  chain 'A' and resid 451 through 455
      removed outlier: 4.107A  pdb=" N   GLN A 454 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
    Processing helix  chain 'A' and resid 477 through 484
    Processing helix  chain 'A' and resid 488 through 493
    Processing helix  chain 'A' and resid 494 through 504
      removed outlier: 3.575A  pdb=" N   MET A 498 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 534
    Processing helix  chain 'A' and resid 549 through 578
      removed outlier: 3.976A  pdb=" N   VAL A 569 " --> pdb=" O   GLU A 565 " (cutoff:3.500A)
      Proline residue:  A 572  - end of helix
    Processing helix  chain 'A' and resid 581 through 589
    Processing helix  chain 'A' and resid 590 through 595
      removed outlier: 3.581A  pdb=" N   PHE A 595 " --> pdb=" O   PRO A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 597
      No H-bonds generated for 'chain 'A' and resid 596 through 597'
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 605 through 623
    Processing helix  chain 'A' and resid 625 through 640
    Processing helix  chain 'A' and resid 646 through 673
      removed outlier: 3.928A  pdb=" N   ASP A 671 " --> pdb=" O   ARG A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 701
      removed outlier: 4.031A  pdb=" N   ALA A 700 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 722
    Processing helix  chain 'A' and resid 726 through 749
      removed outlier: 3.572A  pdb=" N   LYS A 747 " --> pdb=" O   TRP A 743 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 776
      removed outlier: 3.522A  pdb=" N   LEU A 758 " --> pdb=" O   THR A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 798
    Processing helix  chain 'A' and resid 799 through 804
    Processing helix  chain 'A' and resid 807 through 814
      removed outlier: 3.503A  pdb=" N   GLU A 811 " --> pdb=" O   ASP A 808 " (cutoff:3.500A)
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'A' and resid 818 through 833
    Processing helix  chain 'A' and resid 853 through 874
    Processing helix  chain 'A' and resid 878 through 881
    Processing helix  chain 'A' and resid 882 through 888
    Processing helix  chain 'A' and resid 892 through 911
      removed outlier: 6.868A  pdb=" N   ASP A 898 " --> pdb=" O   ASN A 894 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE A 899 " --> pdb=" O   ASP A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 934
    Processing helix  chain 'A' and resid 942 through 958
    Processing helix  chain 'A' and resid 966 through 982
    Processing helix  chain 'A' and resid 996 through 998
      No H-bonds generated for 'chain 'A' and resid 996 through 998'
    Processing helix  chain 'A' and resid 999 through 1004
    Processing helix  chain 'A' and resid 1005 through 1009
      removed outlier: 4.044A  pdb=" N   SER A1008 " --> pdb=" O   GLU A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1025
      removed outlier: 3.694A  pdb=" N   THR A1017 " --> pdb=" O   GLN A1013 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS A1024 " --> pdb=" O   VAL A1020 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE A1025 " --> pdb=" O   TYR A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1050
      removed outlier: 4.622A  pdb=" N   LEU A1041 " --> pdb=" O   VAL A1037 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 343
    Processing helix  chain 'B' and resid 344 through 348
    Processing helix  chain 'B' and resid 357 through 367
    Processing helix  chain 'B' and resid 368 through 373
    Processing helix  chain 'B' and resid 382 through 391
      removed outlier: 3.640A  pdb=" N   LEU B 388 " --> pdb=" O   ARG B 384 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)

    561 hydrogen bonds defined for protein.
    1641 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: 1.33

  Time building geometry restraints manager: 0.83 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: 2699
        1.35 -     1.47: 936
        1.47 -     1.58: 4649
        1.58 -     1.70: 0
        1.70 -     1.81: 95
  Bond restraints: 8379
  Sorted by residual:
  bond pdb=" N   VAL B 329 "
       pdb=" CA  VAL B 329 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.10e-02 8.26e+03 1.13e+01
  bond pdb=" N   LEU A 571 "
       pdb=" CA  LEU A 571 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 9.20e-03 1.18e+04 1.09e+01
  bond pdb=" N   HIS A 623 "
       pdb=" CA  HIS A 623 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.19e-02 7.06e+03 1.07e+01
  bond pdb=" N   VAL A 814 "
       pdb=" CA  VAL A 814 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.19e-02 7.06e+03 1.06e+01
  bond pdb=" N   VAL A 424 "
       pdb=" CA  VAL A 424 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.21e-02 6.83e+03 1.01e+01
  ... (remaining 8374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 7968
        1.61 -     3.21: 2964
        3.21 -     4.82: 328
        4.82 -     6.43: 28
        6.43 -     8.03: 8
  Bond angle restraints: 11296
  Sorted by residual:
  angle pdb=" CA  ASP A 193 "
        pdb=" CB  ASP A 193 "
        pdb=" CG  ASP A 193 "
      ideal   model   delta    sigma   weight residual
     112.60  119.25   -6.65 1.00e+00 1.00e+00 4.42e+01
  angle pdb=" N   GLU A1035 "
        pdb=" CA  GLU A1035 "
        pdb=" C   GLU A1035 "
      ideal   model   delta    sigma   weight residual
     113.16  105.79    7.37 1.24e+00 6.50e-01 3.53e+01
  angle pdb=" CA  ASP B 343 "
        pdb=" CB  ASP B 343 "
        pdb=" CG  ASP B 343 "
      ideal   model   delta    sigma   weight residual
     112.60  117.66   -5.06 1.00e+00 1.00e+00 2.56e+01
  angle pdb=" CA  PHE A 595 "
        pdb=" CB  PHE A 595 "
        pdb=" CG  PHE A 595 "
      ideal   model   delta    sigma   weight residual
     113.80  118.62   -4.82 1.00e+00 1.00e+00 2.32e+01
  angle pdb=" C   TYR A 479 "
        pdb=" CA  TYR A 479 "
        pdb=" CB  TYR A 479 "
      ideal   model   delta    sigma   weight residual
     110.85  118.88   -8.03 1.70e+00 3.46e-01 2.23e+01
  ... (remaining 11291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.22: 4521
       13.22 -    26.43: 365
       26.43 -    39.65: 149
       39.65 -    52.87: 19
       52.87 -    66.08: 73
  Dihedral angle restraints: 5127
    sinusoidal: 2123
      harmonic: 3004
  Sorted by residual:
  dihedral pdb=" CB  LYS A 784 "
           pdb=" CG  LYS A 784 "
           pdb=" CD  LYS A 784 "
           pdb=" CE  LYS A 784 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.22  -59.78     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LYS A 717 "
           pdb=" CA  LYS A 717 "
           pdb=" CB  LYS A 717 "
           pdb=" CG  LYS A 717 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.39  -59.61     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" C   TYR A 479 "
           pdb=" N   TYR A 479 "
           pdb=" CA  TYR A 479 "
           pdb=" CB  TYR A 479 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.27    7.67     0      2.50e+00 1.60e-01 9.40e+00
  ... (remaining 5124 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 507
       0.050 -    0.100: 428
       0.100 -    0.151: 247
       0.151 -    0.201: 95
       0.201 -    0.251: 7
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  PHE A 595 "
            pdb=" N   PHE A 595 "
            pdb=" C   PHE A 595 "
            pdb=" CB  PHE A 595 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  ILE A 646 "
            pdb=" N   ILE A 646 "
            pdb=" C   ILE A 646 "
            pdb=" CB  ILE A 646 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  VAL A  98 "
            pdb=" N   VAL A  98 "
            pdb=" C   VAL A  98 "
            pdb=" CB  VAL A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 614 "    0.274 9.50e-02 1.11e+02   1.23e-01 9.24e+00
        pdb=" NE  ARG A 614 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 614 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 614 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 614 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 953 "   -0.267 9.50e-02 1.11e+02   1.20e-01 8.87e+00
        pdb=" NE  ARG A 953 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 953 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 953 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 953 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 344 "   -0.265 9.50e-02 1.11e+02   1.19e-01 8.66e+00
        pdb=" NE  ARG A 344 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 344 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 344 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 344 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1427 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2794
        2.86 -     3.37: 8184
        3.37 -     3.88: 13325
        3.88 -     4.39: 16144
        4.39 -     4.90: 26314
  Nonbonded interactions: 66761
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 433 "
            pdb=" N   SER A 438 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OH  TYR A 355 "
            pdb=" OG1 THR A 368 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OD2 ASP A 939 "
            pdb=" OG  SER A 941 "
     model   vdw
     2.416 3.040
  nonbonded pdb=" OD1 ASN A 325 "
            pdb=" OG  SER A 327 "
     model   vdw
     2.421 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG1 THR B 336 "
     model   vdw
     2.436 3.040
  ... (remaining 66756 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
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      :  0.013   0.040   8379  Z= 0.954
  Angle     :  1.508   8.033  11296  Z= 1.180
  Chirality :  0.087   0.251   1284
  Planarity :  0.012   0.123   1430
  Dihedral  : 14.190  66.084   3167
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.19 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.86 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.24), residues: 1003
  helix:  0.68 (0.18), residues: 710
  sheet:  None (None), residues: 0
  loop : -1.12 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 541 
 TYR   0.020   0.002   TYR B 344 
 PHE   0.014   0.002   PHE A 120 
 TRP   0.012   0.002   TRP A 168 
 HIS   0.012   0.002   HIS A 421 

Details of bonding type rmsd
  covalent geometry    : bond        0.01278 ( 8379)
  covalent geometry    : angle       1.50789 (11296)
  hydrogen bonds       : bond        0.20747 (  561)
  hydrogen bonds       : angle       5.86427 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 262
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8220 (mm-30) cc_final: 0.6576 (mm-30)
REVERT: A  361 ASN cc_start: 0.6865 (t0) cc_final: 0.6438 (t0)
REVERT: A  515 ASP cc_start: 0.8087 (m-30) cc_final: 0.7799 (t0)
REVERT: A  547 VAL cc_start: 0.8452 (t) cc_final: 0.8097 (p)
REVERT: A  756 GLU cc_start: 0.7416 (tt0) cc_final: 0.7158 (tm-30)
REVERT: A  811 GLU cc_start: 0.7979 (tt0) cc_final: 0.7748 (tt0)
REVERT: A  976 ASP cc_start: 0.8551 (t0) cc_final: 0.8272 (t0)
REVERT: A  979 GLU cc_start: 0.7731 (tt0) cc_final: 0.7423 (tm-30)
  outliers start: 13
  outliers final: 0
  residues processed: 268
  average time/residue: 0.6188
  time to fit residues: 174.2637
Evaluate side-chains
  181 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.1980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
A 277 ASN
A 278 GLN
A 412 ASN
A 454 GLN
A 608 HIS
A 618 ASN
A 735 GLN
A 770 GLN
A 774 HIS
A 786 GLN
** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 GLN
A 928 ASN
A 934 ASN
A 996 ASN
B 382 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.059962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2533 r_free = 0.2533 target = 0.046327 restraints weight = 19517.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.2529 rms_B_bonded: 1.68
r_work: 0.2414 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2306 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8379  Z= 0.166
  Angle     :  0.609   8.478  11296  Z= 0.320
  Chirality :  0.040   0.245   1284
  Planarity :  0.004   0.035   1430
  Dihedral  :  3.911  15.795   1097
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.50 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 17.25 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.26), residues: 1003
  helix:  1.83 (0.18), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.09 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 137 
 TYR   0.024   0.002   TYR A 874 
 PHE   0.020   0.002   PHE A 175 
 TRP   0.021   0.002   TRP A1038 
 HIS   0.005   0.002   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8379)
  covalent geometry    : angle       0.60868 (11296)
  hydrogen bonds       : bond        0.05791 (  561)
  hydrogen bonds       : angle       4.12795 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 196
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8019 (ttm-80)
REVERT: A  151 GLU cc_start: 0.8278 (mp0) cc_final: 0.8011 (mp0)
REVERT: A  273 GLU cc_start: 0.8352 (tt0) cc_final: 0.8001 (tt0)
REVERT: A  547 VAL cc_start: 0.8940 (t) cc_final: 0.8721 (p)
REVERT: A 1016 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7892 (tpm-80)
  outliers start: 39
  outliers final: 11
  residues processed: 214
  average time/residue: 0.6052
  time to fit residues: 136.1658
Evaluate side-chains
  185 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  959 PHE
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1046 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.057005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2446 r_free = 0.2446 target = 0.043248 restraints weight = 19533.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2443 rms_B_bonded: 1.69
r_work: 0.2327 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2218 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8379  Z= 0.206
  Angle     :  0.627   8.791  11296  Z= 0.330
  Chirality :  0.041   0.244   1284
  Planarity :  0.005   0.041   1430
  Dihedral  :  4.064  18.402   1097
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.79 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 17.69 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.26), residues: 1003
  helix:  1.80 (0.18), residues: 719
  sheet:  None (None), residues: 0
  loop :  0.05 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 546 
 TYR   0.023   0.002   TYR A 874 
 PHE   0.023   0.002   PHE A 175 
 TRP   0.025   0.002   TRP A1038 
 HIS   0.006   0.002   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 8379)
  covalent geometry    : angle       0.62744 (11296)
  hydrogen bonds       : bond        0.06335 (  561)
  hydrogen bonds       : angle       4.16364 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 184
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8777 (m-30)
REVERT: A  135 MET cc_start: 0.8296 (mtp) cc_final: 0.7929 (mtp)
REVERT: A  139 MET cc_start: 0.8300 (mmm) cc_final: 0.7659 (mtp)
REVERT: A  146 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8151 (ttm-80)
REVERT: A  151 GLU cc_start: 0.8346 (mp0) cc_final: 0.8060 (mp0)
REVERT: A  227 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8711 (ttm)
REVERT: A  255 MET cc_start: 0.7385 (mmp) cc_final: 0.6224 (ptt)
REVERT: A  547 VAL cc_start: 0.8963 (t) cc_final: 0.8762 (p)
REVERT: A  698 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8138 (t-90)
REVERT: A  976 ASP cc_start: 0.8640 (t0) cc_final: 0.8433 (t0)
  outliers start: 48
  outliers final: 25
  residues processed: 205
  average time/residue: 0.5980
  time to fit residues: 129.2524
Evaluate side-chains
  195 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0370
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 832 HIS
A1046 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.056769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2444 r_free = 0.2444 target = 0.043148 restraints weight = 20073.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2443 rms_B_bonded: 1.73
r_work: 0.2318 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2207 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8379  Z= 0.188
  Angle     :  0.621  10.730  11296  Z= 0.324
  Chirality :  0.039   0.170   1284
  Planarity :  0.005   0.043   1430
  Dihedral  :  4.114  19.731   1097
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.79 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 18.89 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.26), residues: 1003
  helix:  1.85 (0.19), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.03 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1045 
 TYR   0.020   0.002   TYR A 874 
 PHE   0.020   0.002   PHE A 175 
 TRP   0.023   0.002   TRP A1038 
 HIS   0.004   0.001   HIS A 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 8379)
  covalent geometry    : angle       0.62070 (11296)
  hydrogen bonds       : bond        0.05882 (  561)
  hydrogen bonds       : angle       4.16016 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 175
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8219 (ttm-80)
REVERT: A  151 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8041 (mp0)
REVERT: A  227 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8685 (ttm)
REVERT: A  255 MET cc_start: 0.7372 (mmp) cc_final: 0.6240 (ptt)
REVERT: A  273 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8042 (tt0)
REVERT: A  547 VAL cc_start: 0.9013 (t) cc_final: 0.8802 (p)
REVERT: A  698 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8143 (t-90)
REVERT: A  920 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8772 (tp)
REVERT: A  941 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8735 (p)
REVERT: A 1025 PHE cc_start: 0.7173 (m-80) cc_final: 0.6958 (m-80)
  outliers start: 52
  outliers final: 22
  residues processed: 201
  average time/residue: 0.6234
  time to fit residues: 131.9820
Evaluate side-chains
  194 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  151 GLU
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** 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 = 0.2803 r_free = 0.2803 target = 0.056132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2424 r_free = 0.2424 target = 0.042426 restraints weight = 19847.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.2421 rms_B_bonded: 1.67
r_work: 0.2306 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2199 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8379  Z= 0.201
  Angle     :  0.638  12.098  11296  Z= 0.333
  Chirality :  0.041   0.222   1284
  Planarity :  0.005   0.043   1430
  Dihedral  :  4.159  19.137   1097
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.89 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 20.20 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.26), residues: 1003
  helix:  1.83 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.01 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 546 
 TYR   0.019   0.002   TYR B 344 
 PHE   0.035   0.002   PHE A 927 
 TRP   0.025   0.002   TRP A1038 
 HIS   0.005   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 8379)
  covalent geometry    : angle       0.63848 (11296)
  hydrogen bonds       : bond        0.06014 (  561)
  hydrogen bonds       : angle       4.16676 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 168
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8211 (ttm-80)
REVERT: A  150 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7996 (mm-30)
REVERT: A  227 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (ttm)
REVERT: A  255 MET cc_start: 0.7435 (mmp) cc_final: 0.6286 (ptt)
REVERT: A  411 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8413 (mp0)
REVERT: A  547 VAL cc_start: 0.9047 (t) cc_final: 0.8837 (p)
REVERT: A  698 HIS cc_start: 0.9263 (OUTLIER) cc_final: 0.8155 (t-90)
REVERT: A  920 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: A  941 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8776 (p)
  outliers start: 48
  outliers final: 26
  residues processed: 193
  average time/residue: 0.6276
  time to fit residues: 127.7878
Evaluate side-chains
  191 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  411 GLU
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   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  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 780 ASN
A1046 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.055694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2416 r_free = 0.2416 target = 0.042112 restraints weight = 19895.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2412 rms_B_bonded: 1.67
r_work: 0.2298 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2190 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8379  Z= 0.211
  Angle     :  0.659   8.588  11296  Z= 0.348
  Chirality :  0.041   0.207   1284
  Planarity :  0.005   0.045   1430
  Dihedral  :  4.230  19.666   1097
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.09 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 20.52 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.26), residues: 1003
  helix:  1.77 (0.19), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.05 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1045 
 TYR   0.020   0.002   TYR B 344 
 PHE   0.029   0.002   PHE A 927 
 TRP   0.028   0.002   TRP A1038 
 HIS   0.005   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8379)
  covalent geometry    : angle       0.65894 (11296)
  hydrogen bonds       : bond        0.06111 (  561)
  hydrogen bonds       : angle       4.22619 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 164
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8770 (m-30)
REVERT: A  195 TYR cc_start: 0.8599 (t80) cc_final: 0.8344 (t80)
REVERT: A  227 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8681 (ttm)
REVERT: A  246 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7764 (mtm-85)
REVERT: A  255 MET cc_start: 0.7476 (mmp) cc_final: 0.6386 (ptt)
REVERT: A  411 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8353 (mp0)
REVERT: A  547 VAL cc_start: 0.9054 (t) cc_final: 0.8839 (p)
REVERT: A  698 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.8172 (t-90)
REVERT: A  920 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8703 (tp)
REVERT: A  941 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8840 (p)
  outliers start: 52
  outliers final: 26
  residues processed: 192
  average time/residue: 0.5747
  time to fit residues: 116.2890
Evaluate side-chains
  195 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  151 GLU
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  411 GLU
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 96 optimal weight:    0.2980
   chunk 66 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 85 optimal weight:    0.4980
   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  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** 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 = 0.2813 r_free = 0.2813 target = 0.056517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2439 r_free = 0.2439 target = 0.042984 restraints weight = 19957.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2437 rms_B_bonded: 1.67
r_work: 0.2323 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2215 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8379  Z= 0.177
  Angle     :  0.646   9.165  11296  Z= 0.339
  Chirality :  0.039   0.174   1284
  Planarity :  0.005   0.049   1430
  Dihedral  :  4.150  19.162   1097
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.99 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 21.83 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.26), residues: 1003
  helix:  1.91 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -0.04 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 546 
 TYR   0.017   0.002   TYR A 874 
 PHE   0.024   0.002   PHE A 927 
 TRP   0.030   0.002   TRP A1038 
 HIS   0.004   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8379)
  covalent geometry    : angle       0.64574 (11296)
  hydrogen bonds       : bond        0.05554 (  561)
  hydrogen bonds       : angle       4.10164 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.7507 (mmp) cc_final: 0.6450 (ptt)
REVERT: A  273 GLU cc_start: 0.8414 (tt0) cc_final: 0.8035 (tt0)
REVERT: A  411 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8395 (mp0)
REVERT: A  547 VAL cc_start: 0.9050 (t) cc_final: 0.8838 (p)
REVERT: A  698 HIS cc_start: 0.9262 (OUTLIER) cc_final: 0.8144 (t-90)
REVERT: A  920 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8688 (tp)
REVERT: A  941 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8867 (p)
REVERT: A  968 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8557 (mm-30)
REVERT: A 1041 LEU cc_start: 0.8950 (tt) cc_final: 0.8609 (tm)
  outliers start: 42
  outliers final: 25
  residues processed: 187
  average time/residue: 0.6675
  time to fit residues: 131.3257
Evaluate side-chains
  188 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  151 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  411 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  855 ILE
Chi-restraints excluded: chain A residue  890 MET
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  959 PHE
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0670
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.2676

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** 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 = 0.2872 r_free = 0.2872 target = 0.058948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045382 restraints weight = 19938.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2503 rms_B_bonded: 1.66
r_work: 0.2394 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2289 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8379  Z= 0.138
  Angle     :  0.622  10.169  11296  Z= 0.325
  Chirality :  0.037   0.160   1284
  Planarity :  0.005   0.115   1430
  Dihedral  :  3.997  17.616   1097
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.99 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.58 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.27), residues: 1003
  helix:  2.20 (0.19), residues: 729
  sheet:  None (None), residues: 0
  loop :  0.07 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 546 
 TYR   0.015   0.001   TYR A 195 
 PHE   0.030   0.002   PHE A 927 
 TRP   0.029   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8379)
  covalent geometry    : angle       0.62215 (11296)
  hydrogen bonds       : bond        0.04620 (  561)
  hydrogen bonds       : angle       3.93401 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.7892 (m-30) cc_final: 0.7364 (m-30)
REVERT: A  150 GLU cc_start: 0.8372 (pp20) cc_final: 0.8094 (pp20)
REVERT: A  151 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: A  255 MET cc_start: 0.7503 (mmp) cc_final: 0.6490 (ptt)
REVERT: A  273 GLU cc_start: 0.8361 (tt0) cc_final: 0.7987 (tt0)
REVERT: A  547 VAL cc_start: 0.9030 (t) cc_final: 0.8822 (p)
REVERT: A  920 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8635 (tp)
REVERT: A  968 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8548 (mm-30)
  outliers start: 33
  outliers final: 13
  residues processed: 185
  average time/residue: 0.6793
  time to fit residues: 132.1324
Evaluate side-chains
  177 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  890 MET
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 ASN
A 974 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.056347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2433 r_free = 0.2433 target = 0.042770 restraints weight = 19744.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2431 rms_B_bonded: 1.65
r_work: 0.2317 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2209 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8379  Z= 0.196
  Angle     :  0.719  11.248  11296  Z= 0.372
  Chirality :  0.041   0.198   1284
  Planarity :  0.005   0.060   1430
  Dihedral  :  4.196  18.588   1097
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.69 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 24.34 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.27), residues: 1003
  helix:  1.99 (0.19), residues: 727
  sheet:  None (None), residues: 0
  loop :  0.08 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 546 
 TYR   0.022   0.002   TYR A 195 
 PHE   0.018   0.002   PHE A  85 
 TRP   0.030   0.003   TRP A1038 
 HIS   0.005   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8379)
  covalent geometry    : angle       0.71916 (11296)
  hydrogen bonds       : bond        0.05816 (  561)
  hydrogen bonds       : angle       4.11890 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.8474 (pp20) cc_final: 0.8228 (pp20)
REVERT: A  151 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: A  255 MET cc_start: 0.7517 (mmp) cc_final: 0.6479 (ptt)
REVERT: A  273 GLU cc_start: 0.8406 (tt0) cc_final: 0.8038 (tt0)
REVERT: A  547 VAL cc_start: 0.9045 (t) cc_final: 0.8827 (p)
REVERT: A  920 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8700 (tp)
REVERT: A  941 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8873 (p)
REVERT: A  968 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8560 (mm-30)
  outliers start: 29
  outliers final: 17
  residues processed: 179
  average time/residue: 0.6701
  time to fit residues: 125.8334
Evaluate side-chains
  177 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  890 MET
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0870
   chunk 74 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.056342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2432 r_free = 0.2432 target = 0.042737 restraints weight = 19831.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2430 rms_B_bonded: 1.66
r_work: 0.2317 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2209 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8379  Z= 0.199
  Angle     :  0.730  11.694  11296  Z= 0.378
  Chirality :  0.041   0.256   1284
  Planarity :  0.005   0.063   1430
  Dihedral  :  4.253  18.960   1097
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.89 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.78 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.27), residues: 1003
  helix:  1.93 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop :  0.07 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 546 
 TYR   0.018   0.002   TYR B 344 
 PHE   0.018   0.002   PHE A  85 
 TRP   0.026   0.002   TRP A1038 
 HIS   0.004   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8379)
  covalent geometry    : angle       0.73004 (11296)
  hydrogen bonds       : bond        0.05798 (  561)
  hydrogen bonds       : angle       4.17447 ( 1641)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7351 (mpp)
REVERT: A  150 GLU cc_start: 0.8554 (pp20) cc_final: 0.8351 (pp20)
REVERT: A  151 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: A  255 MET cc_start: 0.7529 (mmp) cc_final: 0.6531 (ptt)
REVERT: A  264 LEU cc_start: 0.8121 (mm) cc_final: 0.7560 (mm)
REVERT: A  273 GLU cc_start: 0.8420 (tt0) cc_final: 0.8049 (tt0)
REVERT: A  547 VAL cc_start: 0.9035 (t) cc_final: 0.8815 (p)
REVERT: A  920 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8697 (tp)
REVERT: A  941 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (p)
REVERT: A  968 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8594 (mm-30)
REVERT: A  979 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8335 (mm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 178
  average time/residue: 0.6509
  time to fit residues: 121.7344
Evaluate side-chains
  176 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  124 CYS
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  497 CYS
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  607 LYS
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  890 MET
Chi-restraints excluded: chain A residue  920 ILE
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  350 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** 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 = 0.2805 r_free = 0.2805 target = 0.056000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2423 r_free = 0.2423 target = 0.042381 restraints weight = 19960.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2422 rms_B_bonded: 1.66
r_work: 0.2308 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2202 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8379  Z= 0.212
  Angle     :  0.758  11.141  11296  Z= 0.391
  Chirality :  0.042   0.236   1284
  Planarity :  0.005   0.063   1430
  Dihedral  :  4.358  19.207   1097
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.99 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.89 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.27), residues: 1003
  helix:  1.84 (0.19), residues: 727
  sheet:  None (None), residues: 0
  loop :  0.04 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 546 
 TYR   0.020   0.002   TYR B 344 
 PHE   0.018   0.002   PHE A  85 
 TRP   0.026   0.003   TRP A 168 
 HIS   0.005   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 8379)
  covalent geometry    : angle       0.75788 (11296)
  hydrogen bonds       : bond        0.06025 (  561)
  hydrogen bonds       : angle       4.24977 ( 1641)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3343.24 seconds
wall clock time: 57 minutes 34.93 seconds (3454.93 seconds total)