Starting phenix.real_space_refine
on Wed Mar  4 00:45:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q60_13848/03_2026/7q60_13848.map"
  }
  resolution = 3.13
  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=  -0.001 sd=   0.012
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      46      5.16       5
     C    6047      2.51       5
     N    1554      2.21       5
     O    1803      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9450
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1212, 9450
          Classifications: {'peptide': 1212}
          Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1148}
          Chain breaks: 4
  Time building chain proxies: 2.18, per 1000 atoms: 0.23
  Number of scatterers: 9450
  At special positions: 0
  Unit cell: (111.526, 87.2329, 126.985, 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      46     16.00
     O    1803      8.00
     N    1554      7.00
     C    6047      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  40 " - pdb=" SG  CYS A  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 279 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 464 " - pdb=" SG  CYS A 557 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 589 " - pdb=" SG  CYS A 769 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 633 " - pdb=" SG  CYS A 694 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 819 " - pdb=" SG  CYS A 847 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 845 " - pdb=" SG  CYS A 881 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 919 " - pdb=" SG  CYS A1307 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1075 " - pdb=" SG  CYS A1123 " distance=2.03

  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: 0.76
  Conformation dependent library (CDL) restraints added in 483.0 milliseconds
  

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2256

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 18 sheets defined
      16.3% alpha, 34.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 176 through 178
      No H-bonds generated for 'chain 'A' and resid 176 through 178'
    Processing helix  chain 'A' and resid 596 through 602
      removed outlier: 3.526A  pdb=" N   ARG A 602 " --> pdb=" O   VAL A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 615
      removed outlier: 3.757A  pdb=" N   MET A 615 " --> pdb=" O   SER A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 677
    Processing helix  chain 'A' and resid 880 through 884
      removed outlier: 3.957A  pdb=" N   GLY A 883 " --> pdb=" O   PRO A 880 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLN A 884 " --> pdb=" O   CYS A 881 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 880 through 884'
    Processing helix  chain 'A' and resid 956 through 962
      removed outlier: 3.604A  pdb=" N   LEU A 960 " --> pdb=" O   ALA A 956 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASP A 961 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 965
      No H-bonds generated for 'chain 'A' and resid 963 through 965'
    Processing helix  chain 'A' and resid 972 through 979
    Processing helix  chain 'A' and resid 979 through 990
      removed outlier: 4.458A  pdb=" N   TYR A 983 " --> pdb=" O   ALA A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1015
      removed outlier: 3.848A  pdb=" N   GLN A1011 " --> pdb=" O   GLU A1007 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET A1015 " --> pdb=" O   GLN A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1047
    Processing helix  chain 'A' and resid 1056 through 1067
      removed outlier: 3.547A  pdb=" N   GLN A1060 " --> pdb=" O   PRO A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1102
    Processing helix  chain 'A' and resid 1103 through 1107
      removed outlier: 3.789A  pdb=" N   LEU A1106 " --> pdb=" O   ALA A1103 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU A1107 " --> pdb=" O   ALA A1104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1103 through 1107'
    Processing helix  chain 'A' and resid 1115 through 1122
    Processing helix  chain 'A' and resid 1132 through 1146
      removed outlier: 3.606A  pdb=" N   THR A1136 " --> pdb=" O   THR A1132 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A1146 " --> pdb=" O   TYR A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1159
      removed outlier: 3.620A  pdb=" N   GLN A1159 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1192 through 1205
    Processing helix  chain 'A' and resid 1211 through 1227
    Processing helix  chain 'A' and resid 1240 through 1255
      removed outlier: 3.731A  pdb=" N   ALA A1255 " --> pdb=" O   TYR A1251 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82
      removed outlier: 7.992A  pdb=" N   LYS A  38 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31
      removed outlier: 6.591A  pdb=" N   LEU A  56 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   LYS A  64 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126
    Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131
      removed outlier: 4.346A  pdb=" N   THR A 205 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   SER A 156 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223
    Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230
      removed outlier: 6.671A  pdb=" N   LEU A 229 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 346
      removed outlier: 4.047A  pdb=" N   GLU A 345 " --> pdb=" O   LYS A 360 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   LYS A 360 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351
      removed outlier: 3.553A  pdb=" N   TYR A 351 " --> pdb=" O   ARG A 443 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 456
      removed outlier: 4.617A  pdb=" N   LEU A 471 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507
      removed outlier: 5.966A  pdb=" N   SER A 488 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE A 539 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567
    Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571
      removed outlier: 3.512A  pdb=" N   GLN A 571 " --> pdb=" O   THR A 785 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738
      removed outlier: 7.783A  pdb=" N   THR A 736 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ASP A 595 " --> pdb=" O   THR A 736 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 738 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730
      removed outlier: 3.628A  pdb=" N   ILE A 898 " --> pdb=" O   ARG A 730 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730
      removed outlier: 3.628A  pdb=" N   ILE A 898 " --> pdb=" O   ARG A 730 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795
    Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918
    Processing sheet with id=AB9, first strand: chain 'A' and resid 925 through 930

    392 hydrogen bonds defined for protein.
    1089 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: 2.18

  Time building geometry restraints manager: 1.03 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: 3031
        1.35 -     1.47: 2260
        1.47 -     1.59: 4299
        1.59 -     1.71: 4
        1.71 -     1.83: 69
  Bond restraints: 9663
  Sorted by residual:
  bond pdb=" CG  PRO A 133 "
       pdb=" CD  PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.503  1.304  0.199 3.40e-02 8.65e+02 3.42e+01
  bond pdb=" CB  PRO A 133 "
       pdb=" CG  PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.492  1.662 -0.170 5.00e-02 4.00e+02 1.16e+01
  bond pdb=" CB  PRO A 400 "
       pdb=" CG  PRO A 400 "
    ideal  model  delta    sigma   weight residual
    1.492  1.660 -0.168 5.00e-02 4.00e+02 1.13e+01
  bond pdb=" N   PRO A 133 "
       pdb=" CD  PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.473  1.519 -0.046 1.40e-02 5.10e+03 1.09e+01
  bond pdb=" CB  PRO A 461 "
       pdb=" CG  PRO A 461 "
    ideal  model  delta    sigma   weight residual
    1.492  1.634 -0.142 5.00e-02 4.00e+02 8.03e+00
  ... (remaining 9658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.00: 12992
        5.00 -    10.01: 110
       10.01 -    15.01: 26
       15.01 -    20.02: 1
       20.02 -    25.02: 1
  Bond angle restraints: 13130
  Sorted by residual:
  angle pdb=" CA  PRO A 133 "
        pdb=" N   PRO A 133 "
        pdb=" CD  PRO A 133 "
      ideal   model   delta    sigma   weight residual
     112.00   93.89   18.11 1.40e+00 5.10e-01 1.67e+02
  angle pdb=" CB  MET A 966 "
        pdb=" CG  MET A 966 "
        pdb=" SD  MET A 966 "
      ideal   model   delta    sigma   weight residual
     112.70  137.72  -25.02 3.00e+00 1.11e-01 6.96e+01
  angle pdb=" N   PRO A 133 "
        pdb=" CD  PRO A 133 "
        pdb=" CG  PRO A 133 "
      ideal   model   delta    sigma   weight residual
     103.20   90.93   12.27 1.50e+00 4.44e-01 6.70e+01
  angle pdb=" CA  PRO A 400 "
        pdb=" N   PRO A 400 "
        pdb=" CD  PRO A 400 "
      ideal   model   delta    sigma   weight residual
     112.00  102.86    9.14 1.40e+00 5.10e-01 4.26e+01
  angle pdb=" C   VAL A1112 "
        pdb=" N   ASP A1113 "
        pdb=" CA  ASP A1113 "
      ideal   model   delta    sigma   weight residual
     124.82  136.32  -11.50 1.78e+00 3.16e-01 4.17e+01
  ... (remaining 13125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5111
       17.94 -    35.87: 536
       35.87 -    53.81: 124
       53.81 -    71.74: 25
       71.74 -    89.68: 8
  Dihedral angle restraints: 5804
    sinusoidal: 2289
      harmonic: 3515
  Sorted by residual:
  dihedral pdb=" CB  CYS A 919 "
           pdb=" SG  CYS A 919 "
           pdb=" SG  CYS A1307 "
           pdb=" CB  CYS A1307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.22  -80.78     1      1.00e+01 1.00e-02 8.06e+01
  dihedral pdb=" CA  PHE A 616 "
           pdb=" C   PHE A 616 "
           pdb=" N   PRO A 617 "
           pdb=" CA  PRO A 617 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.02  -38.98     0      5.00e+00 4.00e-02 6.08e+01
  dihedral pdb=" CA  PRO A1320 "
           pdb=" C   PRO A1320 "
           pdb=" N   PRO A1321 "
           pdb=" CA  PRO A1321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.08   33.92     0      5.00e+00 4.00e-02 4.60e+01
  ... (remaining 5801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1276
       0.086 -    0.171: 168
       0.171 -    0.257: 35
       0.257 -    0.343: 5
       0.343 -    0.428: 4
  Chirality restraints: 1488
  Sorted by residual:
  chirality pdb=" CG  LEU A 601 "
            pdb=" CB  LEU A 601 "
            pdb=" CD1 LEU A 601 "
            pdb=" CD2 LEU A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.16   -0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" CB  VAL A 627 "
            pdb=" CA  VAL A 627 "
            pdb=" CG1 VAL A 627 "
            pdb=" CG2 VAL A 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CB  ILE A  96 "
            pdb=" CA  ILE A  96 "
            pdb=" CG1 ILE A  96 "
            pdb=" CG2 ILE A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.25e+00
  ... (remaining 1485 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 132 "   -0.129 5.00e-02 4.00e+02   1.76e-01 4.96e+01
        pdb=" N   PRO A 133 "    0.303 5.00e-02 4.00e+02
        pdb=" CA  PRO A 133 "   -0.092 5.00e-02 4.00e+02
        pdb=" CD  PRO A 133 "   -0.083 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1320 "    0.083 5.00e-02 4.00e+02   1.23e-01 2.43e+01
        pdb=" N   PRO A1321 "   -0.213 5.00e-02 4.00e+02
        pdb=" CA  PRO A1321 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A1321 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 460 "   -0.073 5.00e-02 4.00e+02   1.05e-01 1.76e+01
        pdb=" N   PRO A 461 "    0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO A 461 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 461 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2272
        2.80 -     3.32: 7503
        3.32 -     3.85: 15923
        3.85 -     4.37: 17115
        4.37 -     4.90: 30864
  Nonbonded interactions: 73677
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  58 "
            pdb=" OE2 GLU A  92 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER A1145 "
            pdb=" OG1 THR A1206 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR A 143 "
            pdb=" OH  TYR A 155 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ALA A 827 "
            pdb=" OH  TYR A 832 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OD1 ASN A  22 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.333 3.040
  ... (remaining 73672 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.980
  Find NCS groups from input model:        0.040
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
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      :  0.007   0.199   9673  Z= 0.286
  Angle     :  1.265  25.022  13150  Z= 0.652
  Chirality :  0.066   0.428   1488
  Planarity :  0.011   0.176   1690
  Dihedral  : 15.638  89.678   3518
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 17.70 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.17 %
    Twisted General : 0.09 %

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: -2.64 (0.22), residues: 1202
  helix: -3.24 (0.24), residues: 192
  sheet: -0.26 (0.23), residues: 498
  loop : -2.66 (0.23), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 602 
 TYR   0.046   0.003   TYR A 537 
 PHE   0.052   0.004   PHE A1286 
 TRP   0.030   0.002   TRP A1173 
 HIS   0.007   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 9663)
  covalent geometry    : angle       1.26432 (13130)
  SS BOND              : bond        0.00338 (   10)
  SS BOND              : angle       1.38223 (   20)
  hydrogen bonds       : bond        0.10887 (  383)
  hydrogen bonds       : angle       7.03483 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 PHE cc_start: 0.8242 (m-10) cc_final: 0.8037 (m-10)
REVERT: A  555 GLU cc_start: 0.8044 (pp20) cc_final: 0.7483 (tp30)
REVERT: A  766 MET cc_start: 0.8157 (tmm) cc_final: 0.7777 (ppp)
  outliers start: 6
  outliers final: 3
  residues processed: 114
  average time/residue: 0.0905
  time to fit residues: 15.1791
Evaluate side-chains
  109 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue 1136 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0050
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
A  75 HIS
A 161 GLN
A1069 ASN
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1154 ASN
A1159 GLN
A1277 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.147961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.114547 restraints weight = 21685.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 4.53
r_work: 0.3683 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   9673  Z= 0.171
  Angle     :  0.649  10.123  13150  Z= 0.328
  Chirality :  0.044   0.238   1488
  Planarity :  0.006   0.083   1690
  Dihedral  :  5.353  33.586   1296
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.66 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.27 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -1.94 (0.23), residues: 1202
  helix: -1.63 (0.33), residues: 202
  sheet: -0.19 (0.23), residues: 498
  loop : -2.24 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1274 
 TYR   0.016   0.001   TYR A1135 
 PHE   0.032   0.002   PHE A1286 
 TRP   0.009   0.001   TRP A 619 
 HIS   0.002   0.001   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9663)
  covalent geometry    : angle       0.64874 (13130)
  SS BOND              : bond        0.00198 (   10)
  SS BOND              : angle       0.95813 (   20)
  hydrogen bonds       : bond        0.03470 (  383)
  hydrogen bonds       : angle       5.72746 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 108
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  536 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8543 (mp)
REVERT: A  555 GLU cc_start: 0.7893 (pp20) cc_final: 0.7554 (pp20)
REVERT: A  610 ARG cc_start: 0.8046 (tpm170) cc_final: 0.7760 (tpm170)
REVERT: A  731 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (pm20)
REVERT: A  766 MET cc_start: 0.8326 (tmm) cc_final: 0.7963 (ppp)
REVERT: A 1066 MET cc_start: 0.6144 (pmm) cc_final: 0.5488 (mpp)
REVERT: A 1108 MET cc_start: 0.5736 (mpp) cc_final: 0.5479 (mpp)
  outliers start: 39
  outliers final: 25
  residues processed: 133
  average time/residue: 0.0803
  time to fit residues: 16.1219
Evaluate side-chains
  124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 166 ASN
A 854 HIS
A 986 GLN
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.141868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.105232 restraints weight = 21838.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 4.13
r_work: 0.3598 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   9673  Z= 0.267
  Angle     :  0.710  14.538  13150  Z= 0.361
  Chirality :  0.046   0.176   1488
  Planarity :  0.005   0.058   1690
  Dihedral  :  5.493  32.873   1294
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.49 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 17.51 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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 (0.23), residues: 1202
  helix: -1.12 (0.34), residues: 196
  sheet: -0.40 (0.23), residues: 497
  loop : -2.11 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1274 
 TYR   0.031   0.002   TYR A1135 
 PHE   0.028   0.002   PHE A1286 
 TRP   0.012   0.002   TRP A1173 
 HIS   0.004   0.001   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 9663)
  covalent geometry    : angle       0.70922 (13130)
  SS BOND              : bond        0.00303 (   10)
  SS BOND              : angle       1.11848 (   20)
  hydrogen bonds       : bond        0.03621 (  383)
  hydrogen bonds       : angle       5.79937 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 98
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  464 CYS cc_start: 0.4960 (OUTLIER) cc_final: 0.4665 (p)
REVERT: A  522 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6756 (mm)
REVERT: A  536 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8597 (mt)
REVERT: A  601 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8787 (mm)
REVERT: A  610 ARG cc_start: 0.8020 (tpm170) cc_final: 0.7699 (tpm170)
REVERT: A  733 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6572 (p90)
REVERT: A  766 MET cc_start: 0.8019 (tmm) cc_final: 0.7680 (ppp)
REVERT: A  977 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7432 (pp)
REVERT: A 1066 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5577 (mpp)
REVERT: A 1108 MET cc_start: 0.5670 (mpp) cc_final: 0.5458 (mpp)
REVERT: A 1272 PHE cc_start: 0.7948 (t80) cc_final: 0.7734 (t80)
  outliers start: 49
  outliers final: 29
  residues processed: 135
  average time/residue: 0.0760
  time to fit residues: 15.5692
Evaluate side-chains
  130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1232 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0970
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 986 GLN
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.144897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108978 restraints weight = 22005.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 4.07
r_work: 0.3618 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9673  Z= 0.156
  Angle     :  0.616   8.845  13150  Z= 0.313
  Chirality :  0.044   0.189   1488
  Planarity :  0.004   0.043   1690
  Dihedral  :  5.130  30.186   1294
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 17.32 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -1.61 (0.24), residues: 1202
  helix: -0.62 (0.37), residues: 200
  sheet: -0.34 (0.23), residues: 497
  loop : -1.96 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1274 
 TYR   0.016   0.001   TYR A1135 
 PHE   0.035   0.002   PHE A 978 
 TRP   0.017   0.001   TRP A1173 
 HIS   0.002   0.001   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9663)
  covalent geometry    : angle       0.61563 (13130)
  SS BOND              : bond        0.00186 (   10)
  SS BOND              : angle       0.94837 (   20)
  hydrogen bonds       : bond        0.03121 (  383)
  hydrogen bonds       : angle       5.52774 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 100
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7435 (m-30)
REVERT: A  501 MET cc_start: 0.8228 (ttt) cc_final: 0.8018 (ttt)
REVERT: A  522 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6931 (mm)
REVERT: A  536 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8545 (mp)
REVERT: A  537 TYR cc_start: 0.8632 (p90) cc_final: 0.8300 (p90)
REVERT: A  555 GLU cc_start: 0.8026 (pp20) cc_final: 0.7472 (pp20)
REVERT: A  601 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8768 (mm)
REVERT: A  610 ARG cc_start: 0.7954 (tpm170) cc_final: 0.7531 (tpm170)
REVERT: A  733 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6854 (p90)
REVERT: A  766 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7642 (ppp)
REVERT: A  977 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7439 (pp)
REVERT: A 1066 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5586 (mpp)
REVERT: A 1272 PHE cc_start: 0.7949 (t80) cc_final: 0.7683 (t80)
REVERT: A 1274 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8207 (mmm160)
  outliers start: 48
  outliers final: 29
  residues processed: 133
  average time/residue: 0.0729
  time to fit residues: 14.6501
Evaluate side-chains
  133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.142872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.106832 restraints weight = 22323.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 4.08
r_work: 0.3584 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9673  Z= 0.217
  Angle     :  0.659  15.057  13150  Z= 0.332
  Chirality :  0.045   0.193   1488
  Planarity :  0.004   0.045   1690
  Dihedral  :  5.226  31.166   1294
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.99 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 17.13 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -1.60 (0.24), residues: 1202
  helix: -0.53 (0.36), residues: 199
  sheet: -0.43 (0.23), residues: 496
  loop : -1.87 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1274 
 TYR   0.016   0.002   TYR A1135 
 PHE   0.026   0.002   PHE A1286 
 TRP   0.020   0.002   TRP A1173 
 HIS   0.003   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 9663)
  covalent geometry    : angle       0.65790 (13130)
  SS BOND              : bond        0.00263 (   10)
  SS BOND              : angle       1.00071 (   20)
  hydrogen bonds       : bond        0.03297 (  383)
  hydrogen bonds       : angle       5.58434 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 104
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  114 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8330 (tp)
REVERT: A  162 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7475 (m-30)
REVERT: A  342 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.6171 (ppp)
REVERT: A  464 CYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4642 (p)
REVERT: A  501 MET cc_start: 0.8259 (ttt) cc_final: 0.8034 (ttt)
REVERT: A  536 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8559 (mt)
REVERT: A  601 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (mm)
REVERT: A  610 ARG cc_start: 0.8015 (tpm170) cc_final: 0.7729 (tpm170)
REVERT: A  733 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7140 (p90)
REVERT: A  766 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7678 (ppp)
REVERT: A  796 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.9003 (pp)
REVERT: A 1016 TYR cc_start: 0.6797 (m-80) cc_final: 0.6444 (m-80)
REVERT: A 1066 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5360 (mpp)
REVERT: A 1069 ASN cc_start: 0.6917 (m110) cc_final: 0.6486 (m110)
REVERT: A 1108 MET cc_start: 0.5416 (mpp) cc_final: 0.5096 (mpp)
REVERT: A 1274 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8113 (mmm160)
  outliers start: 57
  outliers final: 32
  residues processed: 144
  average time/residue: 0.0759
  time to fit residues: 16.6331
Evaluate side-chains
  137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 94
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 80 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0370
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1159 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.143647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.107802 restraints weight = 22063.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 4.03
r_work: 0.3606 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9673  Z= 0.172
  Angle     :  0.642  16.728  13150  Z= 0.320
  Chirality :  0.044   0.196   1488
  Planarity :  0.004   0.046   1690
  Dihedral  :  5.069  30.554   1294
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 17.79 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -1.51 (0.24), residues: 1202
  helix: -0.41 (0.37), residues: 200
  sheet: -0.37 (0.23), residues: 497
  loop : -1.84 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1274 
 TYR   0.014   0.001   TYR A1135 
 PHE   0.034   0.002   PHE A1286 
 TRP   0.022   0.001   TRP A1173 
 HIS   0.002   0.001   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9663)
  covalent geometry    : angle       0.64169 (13130)
  SS BOND              : bond        0.00204 (   10)
  SS BOND              : angle       0.90274 (   20)
  hydrogen bonds       : bond        0.03083 (  383)
  hydrogen bonds       : angle       5.42184 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 105
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7526 (m-30)
REVERT: A  339 MET cc_start: 0.6909 (tmm) cc_final: 0.6480 (tmm)
REVERT: A  342 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6223 (ppp)
REVERT: A  464 CYS cc_start: 0.4813 (OUTLIER) cc_final: 0.4469 (p)
REVERT: A  536 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8586 (mt)
REVERT: A  537 TYR cc_start: 0.8583 (p90) cc_final: 0.8339 (p90)
REVERT: A  601 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8771 (mm)
REVERT: A  610 ARG cc_start: 0.7963 (tpm170) cc_final: 0.7627 (tpm170)
REVERT: A  680 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: A  733 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7127 (p90)
REVERT: A  766 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7640 (ppp)
REVERT: A 1066 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5515 (mpp)
REVERT: A 1069 ASN cc_start: 0.6942 (m110) cc_final: 0.6498 (m110)
REVERT: A 1274 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8102 (mmm160)
  outliers start: 52
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0757
  time to fit residues: 16.4227
Evaluate side-chains
  140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1287 GLN
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 119 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 86 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.144819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.109040 restraints weight = 21937.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 4.06
r_work: 0.3623 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9673  Z= 0.130
  Angle     :  0.618  13.316  13150  Z= 0.306
  Chirality :  0.044   0.191   1488
  Planarity :  0.004   0.047   1690
  Dihedral  :  4.860  29.460   1294
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 18.74 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    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: -1.33 (0.24), residues: 1202
  helix: -0.16 (0.38), residues: 197
  sheet: -0.27 (0.23), residues: 494
  loop : -1.75 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1274 
 TYR   0.012   0.001   TYR A1142 
 PHE   0.026   0.001   PHE A 978 
 TRP   0.021   0.001   TRP A1173 
 HIS   0.001   0.000   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9663)
  covalent geometry    : angle       0.61727 (13130)
  SS BOND              : bond        0.00166 (   10)
  SS BOND              : angle       0.81441 (   20)
  hydrogen bonds       : bond        0.02868 (  383)
  hydrogen bonds       : angle       5.27322 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 102
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7426 (m-30)
REVERT: A  177 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7776 (pm20)
REVERT: A  339 MET cc_start: 0.6927 (tmm) cc_final: 0.6485 (tmm)
REVERT: A  464 CYS cc_start: 0.4783 (OUTLIER) cc_final: 0.4560 (p)
REVERT: A  536 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: A  610 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7647 (tpm170)
REVERT: A  732 TYR cc_start: 0.6599 (p90) cc_final: 0.6394 (p90)
REVERT: A  733 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (p90)
REVERT: A  766 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7619 (ppp)
REVERT: A 1066 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5546 (mpp)
REVERT: A 1069 ASN cc_start: 0.7078 (m110) cc_final: 0.6651 (m110)
REVERT: A 1215 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.4784 (mt)
REVERT: A 1274 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8119 (mmm160)
REVERT: A 1288 GLN cc_start: 0.8542 (pp30) cc_final: 0.7993 (pp30)
  outliers start: 46
  outliers final: 29
  residues processed: 135
  average time/residue: 0.0788
  time to fit residues: 15.9918
Evaluate side-chains
  134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 96
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1287 GLN
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 108 optimal weight:    0.5980
   chunk 113 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.143183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.107268 restraints weight = 21992.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 4.03
r_work: 0.3599 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9673  Z= 0.183
  Angle     :  0.649  11.719  13150  Z= 0.321
  Chirality :  0.045   0.257   1488
  Planarity :  0.004   0.047   1690
  Dihedral  :  4.978  30.498   1294
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.82 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 19.12 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -1.32 (0.24), residues: 1202
  helix: -0.06 (0.38), residues: 193
  sheet: -0.32 (0.23), residues: 495
  loop : -1.69 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1274 
 TYR   0.014   0.001   TYR A1142 
 PHE   0.038   0.002   PHE A1286 
 TRP   0.024   0.001   TRP A1173 
 HIS   0.002   0.001   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 9663)
  covalent geometry    : angle       0.64829 (13130)
  SS BOND              : bond        0.00219 (   10)
  SS BOND              : angle       0.89786 (   20)
  hydrogen bonds       : bond        0.03047 (  383)
  hydrogen bonds       : angle       5.37185 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 98
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7522 (m-30)
REVERT: A  177 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7846 (pm20)
REVERT: A  339 MET cc_start: 0.6929 (tmm) cc_final: 0.6473 (tmm)
REVERT: A  342 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6141 (ppp)
REVERT: A  464 CYS cc_start: 0.4782 (OUTLIER) cc_final: 0.4523 (p)
REVERT: A  536 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8648 (mp)
REVERT: A  610 ARG cc_start: 0.7983 (tpm170) cc_final: 0.7643 (tpm170)
REVERT: A  680 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8346 (mp)
REVERT: A  766 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7646 (ppp)
REVERT: A 1016 TYR cc_start: 0.7221 (m-80) cc_final: 0.6762 (m-80)
REVERT: A 1274 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8077 (mmm160)
REVERT: A 1288 GLN cc_start: 0.8579 (pp30) cc_final: 0.8026 (pp30)
  outliers start: 48
  outliers final: 34
  residues processed: 132
  average time/residue: 0.0756
  time to fit residues: 15.1476
Evaluate side-chains
  138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 96
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1287 GLN
Chi-restraints excluded: chain A residue 1307 CYS
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0010
   chunk 118 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.145221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.109569 restraints weight = 21920.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 4.03
r_work: 0.3635 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9673  Z= 0.119
  Angle     :  0.627  10.630  13150  Z= 0.307
  Chirality :  0.044   0.217   1488
  Planarity :  0.004   0.047   1690
  Dihedral  :  4.778  28.984   1294
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.91 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 20.17 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    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: -1.16 (0.24), residues: 1202
  helix:  0.19 (0.38), residues: 190
  sheet: -0.22 (0.23), residues: 494
  loop : -1.64 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1274 
 TYR   0.013   0.001   TYR A1142 
 PHE   0.017   0.001   PHE A1286 
 TRP   0.025   0.001   TRP A1173 
 HIS   0.001   0.000   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9663)
  covalent geometry    : angle       0.62679 (13130)
  SS BOND              : bond        0.00159 (   10)
  SS BOND              : angle       0.77297 (   20)
  hydrogen bonds       : bond        0.02756 (  383)
  hydrogen bonds       : angle       5.18163 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7453 (m-30)
REVERT: A  339 MET cc_start: 0.6953 (tmm) cc_final: 0.6464 (tmm)
REVERT: A  536 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8651 (mp)
REVERT: A  610 ARG cc_start: 0.7932 (tpm170) cc_final: 0.7580 (tpm170)
REVERT: A  680 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8154 (mp)
REVERT: A  766 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7642 (ppp)
REVERT: A 1274 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8059 (mmm160)
REVERT: A 1288 GLN cc_start: 0.8500 (pp30) cc_final: 0.7969 (pp30)
  outliers start: 38
  outliers final: 30
  residues processed: 128
  average time/residue: 0.0752
  time to fit residues: 14.4021
Evaluate side-chains
  126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1287 GLN
Chi-restraints excluded: chain A residue 1307 CYS
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0050
   chunk 74 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 120 optimal weight:    4.9990
   chunk 65 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.145469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.110044 restraints weight = 21771.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 4.01
r_work: 0.3643 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9673  Z= 0.118
  Angle     :  0.624  10.623  13150  Z= 0.305
  Chirality :  0.044   0.212   1488
  Planarity :  0.004   0.047   1690
  Dihedral  :  4.692  28.136   1294
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.49 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.46 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    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: -1.07 (0.24), residues: 1202
  helix:  0.30 (0.39), residues: 190
  sheet: -0.16 (0.24), residues: 494
  loop : -1.61 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 730 
 TYR   0.014   0.001   TYR A1142 
 PHE   0.032   0.001   PHE A1286 
 TRP   0.023   0.001   TRP A1173 
 HIS   0.001   0.000   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9663)
  covalent geometry    : angle       0.62355 (13130)
  SS BOND              : bond        0.00146 (   10)
  SS BOND              : angle       0.69521 (   20)
  hydrogen bonds       : bond        0.02712 (  383)
  hydrogen bonds       : angle       5.09912 ( 1089)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7436 (m-30)
REVERT: A  339 MET cc_start: 0.6936 (tmm) cc_final: 0.6443 (tmm)
REVERT: A  536 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8654 (mp)
REVERT: A  555 GLU cc_start: 0.8175 (pp20) cc_final: 0.7680 (pp20)
REVERT: A  610 ARG cc_start: 0.7962 (tpm170) cc_final: 0.7616 (tpm170)
REVERT: A  680 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (mp)
REVERT: A  733 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6955 (p90)
REVERT: A  766 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7674 (ppp)
REVERT: A  975 MET cc_start: 0.0230 (tmm) cc_final: -0.0297 (tpt)
REVERT: A 1274 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8069 (mmm160)
  outliers start: 37
  outliers final: 30
  residues processed: 125
  average time/residue: 0.0797
  time to fit residues: 15.1124
Evaluate side-chains
  127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1152 ILE
Chi-restraints excluded: chain A residue 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
Chi-restraints excluded: chain A residue 1274 ARG
Chi-restraints excluded: chain A residue 1287 GLN
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1307 CYS
Chi-restraints excluded: chain A residue 1312 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 115 optimal weight:    0.2980
   chunk 87 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 95 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.144137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.108553 restraints weight = 21758.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 4.02
r_work: 0.3620 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9673  Z= 0.158
  Angle     :  0.644  12.797  13150  Z= 0.316
  Chirality :  0.044   0.239   1488
  Planarity :  0.004   0.047   1690
  Dihedral  :  4.772  29.236   1294
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.99 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.55 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    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: -1.13 (0.24), residues: 1202
  helix:  0.25 (0.38), residues: 191
  sheet: -0.22 (0.23), residues: 494
  loop : -1.62 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1274 
 TYR   0.019   0.001   TYR A 537 
 PHE   0.022   0.002   PHE A1286 
 TRP   0.023   0.001   TRP A1173 
 HIS   0.002   0.000   HIS A 914 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9663)
  covalent geometry    : angle       0.64408 (13130)
  SS BOND              : bond        0.00194 (   10)
  SS BOND              : angle       0.68631 (   20)
  hydrogen bonds       : bond        0.02850 (  383)
  hydrogen bonds       : angle       5.16113 ( 1089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2624.23 seconds
wall clock time: 45 minutes 44.54 seconds (2744.54 seconds total)