Starting phenix.real_space_refine
on Fri Feb 14 01:52:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_13848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_13848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_13848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_13848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q60_13848/02_2025/7q60_13848.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.012
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.60, per 1000 atoms: 0.59
  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: 2.28
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.35
  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: 4.01

  Time building geometry restraints manager: 2.67 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:             1.150
  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:          0.350
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     24.550
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.110
-------------------------------------------------------------------------------
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   9663  Z= 0.393
  Angle     :  1.264  25.022  13130  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.030   0.002   TRP A1173 
 HIS   0.007   0.001   HIS A 366 
 PHE   0.052   0.004   PHE A1286 
 TYR   0.046   0.003   TYR A 537 
 ARG   0.023   0.001   ARG A 602 

*********************** 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  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 PHE cc_start: 0.8241 (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: 0.2085
  time to fit residues: 34.6090
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  : 1.083 
-------------------------------------------------------------------------------
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 102 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1154 ASN
A1277 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.148722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.115977 restraints weight = 21597.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 4.48
r_work: 0.3718 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9663  Z= 0.222
  Angle     :  0.635   9.464  13130  Z= 0.321
  Chirality :  0.043   0.215   1488
  Planarity :  0.006   0.082   1690
  Dihedral  :  5.344  33.826   1296
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.83 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.23), residues: 1202
  helix: -1.62 (0.33), residues: 202
  sheet: -0.19 (0.24), residues: 494
  loop : -2.23 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1173 
 HIS   0.002   0.001   HIS A1018 
 PHE   0.031   0.002   PHE A1286 
 TYR   0.015   0.001   TYR A 945 
 ARG   0.005   0.000   ARG A1274 

*********************** 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
  144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A  555 GLU cc_start: 0.7918 (pp20) cc_final: 0.7583 (pp20)
REVERT: A  731 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7796 (pm20)
REVERT: A  766 MET cc_start: 0.8372 (tmm) cc_final: 0.8035 (ppp)
REVERT: A  966 MET cc_start: 0.7299 (ppp) cc_final: 0.7089 (ppp)
REVERT: A 1066 MET cc_start: 0.6243 (pmm) cc_final: 0.5605 (mpp)
REVERT: A 1108 MET cc_start: 0.5533 (mpp) cc_final: 0.5284 (mpp)
  outliers start: 34
  outliers final: 19
  residues processed: 133
  average time/residue: 0.1846
  time to fit residues: 36.3670
Evaluate side-chains
  117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  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  472 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  682 ILE
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 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 119 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.2980
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 854 HIS
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1159 GLN
A1204 GLN
A1277 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.143870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.110817 restraints weight = 21928.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 4.65
r_work: 0.3629 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9663  Z= 0.303
  Angle     :  0.664   9.671  13130  Z= 0.335
  Chirality :  0.044   0.172   1488
  Planarity :  0.005   0.057   1690
  Dihedral  :  5.207  32.022   1294
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.22 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.24), residues: 1202
  helix: -0.92 (0.36), residues: 200
  sheet: -0.31 (0.23), residues: 499
  loop : -2.05 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1173 
 HIS   0.004   0.001   HIS A 914 
 PHE   0.025   0.002   PHE A1286 
 TYR   0.026   0.002   TYR A1135 
 ARG   0.005   0.000   ARG A1274 

*********************** 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
  146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 99
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  522 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6801 (mm)
REVERT: A  536 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8709 (mt)
REVERT: A  555 GLU cc_start: 0.7944 (pp20) cc_final: 0.7425 (pp20)
REVERT: A  601 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8715 (mm)
REVERT: A  610 ARG cc_start: 0.7997 (tpm170) cc_final: 0.7717 (tpm170)
REVERT: A  977 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7082 (pp)
REVERT: A 1066 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5517 (mpp)
REVERT: A 1108 MET cc_start: 0.5807 (mpp) cc_final: 0.5590 (mpp)
REVERT: A 1272 PHE cc_start: 0.7964 (t80) cc_final: 0.7679 (t80)
  outliers start: 47
  outliers final: 29
  residues processed: 132
  average time/residue: 0.2004
  time to fit residues: 38.8449
Evaluate side-chains
  122 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 88
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
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  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  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  615 MET
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  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 40 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 115 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 31 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 120 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.146418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.110408 restraints weight = 21880.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 4.16
r_work: 0.3668 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9663  Z= 0.196
  Angle     :  0.607  13.321  13130  Z= 0.304
  Chirality :  0.043   0.194   1488
  Planarity :  0.004   0.041   1690
  Dihedral  :  4.903  29.990   1294
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.83 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.51 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.24), residues: 1202
  helix: -0.49 (0.37), residues: 200
  sheet: -0.22 (0.23), residues: 499
  loop : -1.90 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1173 
 HIS   0.002   0.000   HIS A 914 
 PHE   0.035   0.002   PHE A 978 
 TYR   0.015   0.001   TYR A1135 
 ARG   0.007   0.000   ARG A1274 

*********************** 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
  141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 98
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A  464 CYS cc_start: 0.4741 (OUTLIER) cc_final: 0.4427 (p)
REVERT: A  501 MET cc_start: 0.8250 (ttt) cc_final: 0.7858 (ttt)
REVERT: A  522 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6803 (mm)
REVERT: A  536 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8570 (mp)
REVERT: A  537 TYR cc_start: 0.8610 (p90) cc_final: 0.8340 (p90)
REVERT: A  601 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8729 (mm)
REVERT: A  733 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6091 (p90)
REVERT: A  977 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7143 (pp)
REVERT: A 1066 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5535 (mpp)
REVERT: A 1215 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.4704 (mt)
REVERT: A 1272 PHE cc_start: 0.7931 (t80) cc_final: 0.7661 (t80)
  outliers start: 43
  outliers final: 24
  residues processed: 128
  average time/residue: 0.1733
  time to fit residues: 33.8284
Evaluate side-chains
  125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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  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  536 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  733 PHE
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 1199 TYR
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1235 PHE
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 41 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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
** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1159 GLN
A1277 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.144498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.108655 restraints weight = 21989.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 4.05
r_work: 0.3615 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9663  Z= 0.282
  Angle     :  0.639  14.617  13130  Z= 0.321
  Chirality :  0.044   0.191   1488
  Planarity :  0.004   0.041   1690
  Dihedral  :  5.009  30.778   1294
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.49 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 17.13 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.24), residues: 1202
  helix: -0.41 (0.37), residues: 201
  sheet: -0.23 (0.23), residues: 497
  loop : -1.79 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1173 
 HIS   0.003   0.001   HIS A 914 
 PHE   0.027   0.002   PHE A  33 
 TYR   0.015   0.001   TYR A1135 
 ARG   0.004   0.000   ARG A1274 

*********************** 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
  153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 104
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A  144 MET cc_start: 0.8344 (mmt) cc_final: 0.7734 (mmt)
REVERT: A  162 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7529 (m-30)
REVERT: A  342 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5989 (ppp)
REVERT: A  464 CYS cc_start: 0.4842 (OUTLIER) cc_final: 0.4606 (p)
REVERT: A  501 MET cc_start: 0.8270 (ttt) cc_final: 0.7978 (ttt)
REVERT: A  536 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8626 (mt)
REVERT: A  537 TYR cc_start: 0.8597 (p90) cc_final: 0.8326 (p90)
REVERT: A  601 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8773 (mm)
REVERT: A  610 ARG cc_start: 0.7981 (tpm170) cc_final: 0.7659 (tpm170)
REVERT: A  733 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6971 (p90)
REVERT: A  977 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7365 (pp)
REVERT: A 1066 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5298 (mpp)
REVERT: A 1069 ASN cc_start: 0.6901 (m-40) cc_final: 0.6510 (m110)
REVERT: A 1108 MET cc_start: 0.5360 (mpp) cc_final: 0.5029 (mpp)
  outliers start: 49
  outliers final: 29
  residues processed: 140
  average time/residue: 0.1787
  time to fit residues: 37.8300
Evaluate side-chains
  134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
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  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  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  977 LEU
Chi-restraints excluded: chain A residue 1066 MET
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
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 99 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 396 ASN
A 986 GLN
A1159 GLN
A1277 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.145176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.112507 restraints weight = 21715.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 4.38
r_work: 0.3633 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9663  Z= 0.210
  Angle     :  0.612  15.774  13130  Z= 0.304
  Chirality :  0.044   0.193   1488
  Planarity :  0.004   0.044   1690
  Dihedral  :  4.825  29.986   1294
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.17 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.24), residues: 1202
  helix: -0.21 (0.38), residues: 198
  sheet: -0.14 (0.23), residues: 495
  loop : -1.77 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1173 
 HIS   0.002   0.000   HIS A 914 
 PHE   0.034   0.002   PHE A1286 
 TYR   0.013   0.001   TYR A1135 
 ARG   0.003   0.000   ARG A 610 

*********************** 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
  147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  144 MET cc_start: 0.8355 (mmt) cc_final: 0.8108 (mmt)
REVERT: A  342 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6273 (ppp)
REVERT: A  464 CYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4504 (p)
REVERT: A  536 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8577 (mt)
REVERT: A  537 TYR cc_start: 0.8581 (p90) cc_final: 0.8326 (p90)
REVERT: A  601 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8752 (mm)
REVERT: A  610 ARG cc_start: 0.7923 (tpm170) cc_final: 0.7698 (tpm170)
REVERT: A  732 TYR cc_start: 0.6726 (p90) cc_final: 0.5983 (p90)
REVERT: A  733 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7124 (p90)
REVERT: A 1066 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5336 (mpp)
REVERT: A 1069 ASN cc_start: 0.6938 (m-40) cc_final: 0.6638 (m110)
REVERT: A 1215 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.4783 (mt)
REVERT: A 1288 GLN cc_start: 0.8590 (pp30) cc_final: 0.8071 (pp30)
  outliers start: 43
  outliers final: 30
  residues processed: 135
  average time/residue: 0.1836
  time to fit residues: 37.6488
Evaluate side-chains
  137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
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  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  733 PHE
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 1066 MET
Chi-restraints excluded: chain A residue 1113 ASP
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 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 81 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0870
   chunk 78 optimal weight:    0.0570
   chunk 68 optimal weight:    3.9990
   chunk 91 optimal weight:    8.9990
   chunk 105 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 90 optimal weight:    8.9990
   chunk 87 optimal weight:    0.0470
   overall best weight:    0.2974

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

Flipped N/Q/H residues before XYZ refinement:
A 281 ASN
A1277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.147402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.111903 restraints weight = 21925.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 4.08
r_work: 0.3677 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9663  Z= 0.155
  Angle     :  0.596  16.672  13130  Z= 0.294
  Chirality :  0.043   0.188   1488
  Planarity :  0.004   0.046   1690
  Dihedral  :  4.581  28.228   1294
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.99 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.84 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.24), residues: 1202
  helix: -0.03 (0.38), residues: 198
  sheet:  0.04 (0.24), residues: 479
  loop : -1.73 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1173 
 HIS   0.001   0.000   HIS A 366 
 PHE   0.020   0.001   PHE A1286 
 TYR   0.013   0.001   TYR A1142 
 ARG   0.002   0.000   ARG A1274 

*********************** 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
  144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A   66 LEU cc_start: 0.8167 (tp) cc_final: 0.7932 (mt)
REVERT: A  162 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7132 (m-30)
REVERT: A  342 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6418 (ppp)
REVERT: A  464 CYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4738 (p)
REVERT: A  536 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: A  537 TYR cc_start: 0.8551 (p90) cc_final: 0.8337 (p90)
REVERT: A  610 ARG cc_start: 0.7896 (tpm170) cc_final: 0.7631 (tpm170)
REVERT: A  732 TYR cc_start: 0.6545 (p90) cc_final: 0.5936 (p90)
  outliers start: 37
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1875
  time to fit residues: 37.0876
Evaluate side-chains
  120 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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  137 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  342 MET
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  682 ILE
Chi-restraints excluded: chain A residue  683 LEU
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 1171 ILE
Chi-restraints excluded: chain A residue 1199 TYR
Chi-restraints excluded: chain A residue 1235 PHE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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**
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 = 0.4351 r_free = 0.4351 target = 0.145688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.109827 restraints weight = 22159.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 4.02
r_work: 0.3634 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9663  Z= 0.249
  Angle     :  0.640  14.822  13130  Z= 0.315
  Chirality :  0.044   0.247   1488
  Planarity :  0.004   0.045   1690
  Dihedral  :  4.699  29.145   1294
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.03 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.24), residues: 1202
  helix:  0.06 (0.38), residues: 193
  sheet: -0.06 (0.24), residues: 494
  loop : -1.71 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1173 
 HIS   0.002   0.000   HIS A 914 
 PHE   0.034   0.002   PHE A1286 
 TYR   0.015   0.001   TYR A 798 
 ARG   0.002   0.000   ARG A1274 

*********************** 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
  135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 94
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  298 MET cc_start: 0.7834 (mpp) cc_final: 0.7616 (mpp)
REVERT: A  342 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6395 (ppp)
REVERT: A  464 CYS cc_start: 0.4739 (OUTLIER) cc_final: 0.4510 (p)
REVERT: A  536 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8664 (mp)
REVERT: A  537 TYR cc_start: 0.8530 (p90) cc_final: 0.8327 (p90)
REVERT: A  610 ARG cc_start: 0.7945 (tpm170) cc_final: 0.7644 (tpm170)
REVERT: A 1215 ILE cc_start: 0.5399 (OUTLIER) cc_final: 0.4639 (mt)
  outliers start: 41
  outliers final: 31
  residues processed: 125
  average time/residue: 0.1851
  time to fit residues: 34.4839
Evaluate side-chains
  125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 90
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
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  181 VAL
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  615 MET
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  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 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 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 84 optimal weight:    7.9990
   chunk 98 optimal weight:    0.6980
   chunk 115 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 120 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 92 optimal weight:    9.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4353 r_free = 0.4353 target = 0.145902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.110103 restraints weight = 21836.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 4.04
r_work: 0.3642 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9663  Z= 0.215
  Angle     :  0.639  13.833  13130  Z= 0.314
  Chirality :  0.044   0.235   1488
  Planarity :  0.004   0.045   1690
  Dihedral  :  4.698  28.817   1294
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.03 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.24), residues: 1202
  helix:  0.18 (0.38), residues: 191
  sheet: -0.08 (0.23), residues: 496
  loop : -1.66 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A1173 
 HIS   0.002   0.000   HIS A 914 
 PHE   0.020   0.001   PHE A1286 
 TYR   0.015   0.001   TYR A1142 
 ARG   0.003   0.000   ARG A 602 

*********************** 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
  141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 1.071 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7474 (m-30)
REVERT: A  177 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7735 (pm20)
REVERT: A  298 MET cc_start: 0.7870 (mpp) cc_final: 0.7659 (mpp)
REVERT: A  342 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6485 (ppp)
REVERT: A  464 CYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4729 (p)
REVERT: A  536 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8663 (mp)
REVERT: A  610 ARG cc_start: 0.7946 (tpm170) cc_final: 0.7639 (tpm170)
REVERT: A 1215 ILE cc_start: 0.5447 (OUTLIER) cc_final: 0.4664 (mt)
  outliers start: 41
  outliers final: 32
  residues processed: 131
  average time/residue: 0.1928
  time to fit residues: 38.0551
Evaluate side-chains
  129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 91
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
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  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  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  615 MET
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  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 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 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 104 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.145523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.109719 restraints weight = 22011.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 4.08
r_work: 0.3637 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9663  Z= 0.231
  Angle     :  0.657  13.479  13130  Z= 0.321
  Chirality :  0.044   0.255   1488
  Planarity :  0.004   0.045   1690
  Dihedral  :  4.781  28.803   1294
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.74 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.60 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.24), residues: 1202
  helix:  0.23 (0.38), residues: 191
  sheet: -0.05 (0.23), residues: 488
  loop : -1.69 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A1173 
 HIS   0.002   0.000   HIS A 914 
 PHE   0.034   0.001   PHE A1286 
 TYR   0.018   0.001   TYR A 537 
 ARG   0.003   0.000   ARG A 602 

********************** 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
  129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 91
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7475 (m-30)
REVERT: A  177 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7794 (pm20)
REVERT: A  298 MET cc_start: 0.7862 (mpp) cc_final: 0.7640 (mpp)
REVERT: A  342 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6400 (ppp)
REVERT: A  464 CYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4728 (p)
REVERT: A  536 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8663 (mp)
REVERT: A  610 ARG cc_start: 0.7969 (tpm170) cc_final: 0.7659 (tpm170)
REVERT: A 1215 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.4675 (mt)
  outliers start: 38
  outliers final: 32
  residues processed: 119
  average time/residue: 0.1902
  time to fit residues: 34.6154
Evaluate side-chains
  128 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 90
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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  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  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  615 MET
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  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 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 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 30 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**
** A1137 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 = 0.4322 r_free = 0.4322 target = 0.143571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.107807 restraints weight = 21854.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 4.03
r_work: 0.3605 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9663  Z= 0.292
  Angle     :  0.680  12.834  13130  Z= 0.337
  Chirality :  0.045   0.276   1488
  Planarity :  0.004   0.046   1690
  Dihedral  :  4.997  29.955   1294
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.07 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.79 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1202
  helix:  0.10 (0.38), residues: 191
  sheet: -0.17 (0.23), residues: 490
  loop : -1.68 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1173 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.018   0.002   PHE A1286 
 TYR   0.023   0.002   TYR A 537 
 ARG   0.003   0.000   ARG A 602 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5441.26 seconds
wall clock time: 97 minutes 1.82 seconds (5821.82 seconds total)