Starting phenix.real_space_refine
on Fri Aug 22 19:31:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2025/8i88_35241.cif"
  }
  resolution = 3.7
  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=   0.003 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      23      5.16       5
     C    4714      2.51       5
     N    1210      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7287
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p_pur': 2}
          Link IDs: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 3731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3731
          Classifications: {'peptide': 462}
          Link IDs: {'PTRANS': 23, 'TRANS': 438}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3511
          Classifications: {'peptide': 421}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 408}
  Time building chain proxies: 2.14, per 1000 atoms: 0.29
  Number of scatterers: 7287
  At special positions: 0
  Unit cell: (78.2, 93.5, 125.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P       2     15.00
     O    1338      8.00
     N    1210      7.00
     C    4714      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 446.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1682

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      38.2% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 46 through 60
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 97 through 106
      removed outlier: 3.537A  pdb=" N   PHE B 104 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR B 106 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 132
      removed outlier: 4.081A  pdb=" N   LYS B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 150
      removed outlier: 3.733A  pdb=" N   TYR B 148 " --> pdb=" O   PRO B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.780A  pdb=" N   LEU B 214 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 217
      No H-bonds generated for 'chain 'B' and resid 215 through 217'
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 248 through 265
      removed outlier: 3.676A  pdb=" N   GLY B 265 " --> pdb=" O   PHE B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 350
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 3.990A  pdb=" N   VAL B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR B 377 " --> pdb=" O   PHE B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 477 through 482
      removed outlier: 4.164A  pdb=" N   PHE B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 4.058A  pdb=" N   SER B 493 " --> pdb=" O   ILE B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'C' and resid 14 through 29
      removed outlier: 3.608A  pdb=" N   THR C  18 " --> pdb=" O   ASP C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 56
    Processing helix  chain 'C' and resid 66 through 70
      removed outlier: 3.675A  pdb=" N   ASN C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLN C  70 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 66 through 70'
    Processing helix  chain 'C' and resid 71 through 89
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 4.259A  pdb=" N   ARG C 114 " --> pdb=" O   ILE C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 139
    Processing helix  chain 'C' and resid 146 through 158
      removed outlier: 4.155A  pdb=" N   SER C 150 " --> pdb=" O   ASP C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 203
      removed outlier: 3.520A  pdb=" N   GLU C 202 " --> pdb=" O   ASP C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 231
      removed outlier: 3.533A  pdb=" N   GLU C 231 " --> pdb=" O   PRO C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 249
    Processing helix  chain 'C' and resid 257 through 279
    Processing helix  chain 'C' and resid 300 through 302
      No H-bonds generated for 'chain 'C' and resid 300 through 302'
    Processing helix  chain 'C' and resid 353 through 366
    Processing helix  chain 'C' and resid 369 through 384
      removed outlier: 3.593A  pdb=" N   LEU C 384 " --> pdb=" O   PHE C 380 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.464A  pdb=" N   LYS B   2 " --> pdb=" O   LYS C 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6
    Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20
      removed outlier: 3.599A  pdb=" N   LYS B 270 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 95
      removed outlier: 6.685A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE B  44 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   TRP B 139 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   PHE B 224 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   VAL B 141 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 319
      removed outlier: 7.136A  pdb=" N   CYS B 279 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   HIS B 360 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 281 " --> pdb=" O   HIS B 360 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   VAL B 357 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   VAL B 386 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ILE B 359 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ILE B 388 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ALA B 361 " --> pdb=" O   ILE B 388 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   THR B 387 " --> pdb=" O   ILE B 445 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   ILE B 445 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   SER B 389 " --> pdb=" O   ILE B 443 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   ILE B 443 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   PHE B 419 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   VAL B 412 " --> pdb=" O   PHE B 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319
    Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33
      removed outlier: 5.988A  pdb=" N   ILE C   5 " --> pdb=" O   TRP C  33 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   LYS C   4 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   PHE C  60 " --> pdb=" O   LYS C   4 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   PHE C   6 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   LEU C  62 " --> pdb=" O   PHE C   6 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   SER C   8 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ILE C 118 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 177
      removed outlier: 4.462A  pdb=" N   GLY C 325 " --> pdb=" O   THR C 291 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   THR C 291 " --> pdb=" O   GLY C 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177
    Processing sheet with id=AB1, first strand: chain 'C' and resid 207 through 210
      removed outlier: 3.514A  pdb=" N   LEU C 214 " --> pdb=" O   HIS C 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 304 through 305
    Processing sheet with id=AB3, first strand: chain 'C' and resid 390 through 394

    300 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2276
        1.34 -     1.46: 1811
        1.46 -     1.58: 3349
        1.58 -     1.70: 4
        1.70 -     1.81: 35
  Bond restraints: 7475
  Sorted by residual:
  bond pdb=" CB  PRO C 182 "
       pdb=" CG  PRO C 182 "
    ideal  model  delta    sigma   weight residual
    1.492  1.579 -0.087 5.00e-02 4.00e+02 3.01e+00
  bond pdb=" CG  PRO C 182 "
       pdb=" CD  PRO C 182 "
    ideal  model  delta    sigma   weight residual
    1.503  1.551 -0.048 3.40e-02 8.65e+02 2.01e+00
  bond pdb=" CA  ASP C 100 "
       pdb=" CB  ASP C 100 "
    ideal  model  delta    sigma   weight residual
    1.534  1.557 -0.023 1.76e-02 3.23e+03 1.77e+00
  bond pdb=" C   PHE C 332 "
       pdb=" N   PRO C 333 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.19e-02 7.06e+03 1.50e+00
  bond pdb=" CB  ASP C 107 "
       pdb=" CG  ASP C 107 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.21e+00
  ... (remaining 7470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 10076
        4.02 -     8.05: 28
        8.05 -    12.07: 2
       12.07 -    16.10: 0
       16.10 -    20.12: 1
  Bond angle restraints: 10107
  Sorted by residual:
  angle pdb=" C   PRO C 331 "
        pdb=" N   PHE C 332 "
        pdb=" CA  PHE C 332 "
      ideal   model   delta    sigma   weight residual
     121.80  141.92  -20.12 2.44e+00 1.68e-01 6.80e+01
  angle pdb=" C   LYS C 315 "
        pdb=" CA  LYS C 315 "
        pdb=" CB  LYS C 315 "
      ideal   model   delta    sigma   weight residual
     117.23  110.21    7.02 1.36e+00 5.41e-01 2.66e+01
  angle pdb=" CA  PRO C 182 "
        pdb=" N   PRO C 182 "
        pdb=" CD  PRO C 182 "
      ideal   model   delta    sigma   weight residual
     112.00  105.21    6.79 1.40e+00 5.10e-01 2.35e+01
  angle pdb=" CA  LYS C 315 "
        pdb=" C   LYS C 315 "
        pdb=" N   ASP C 316 "
      ideal   model   delta    sigma   weight residual
     119.98  116.99    2.99 8.50e-01 1.38e+00 1.24e+01
  angle pdb=" N   LEU C  37 "
        pdb=" CA  LEU C  37 "
        pdb=" C   LEU C  37 "
      ideal   model   delta    sigma   weight residual
     114.75  110.45    4.30 1.26e+00 6.30e-01 1.17e+01
  ... (remaining 10102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 3773
       16.65 -    33.31: 513
       33.31 -    49.96: 149
       49.96 -    66.61: 29
       66.61 -    83.26: 7
  Dihedral angle restraints: 4471
    sinusoidal: 1868
      harmonic: 2603
  Sorted by residual:
  dihedral pdb=" CA  TYR C 330 "
           pdb=" C   TYR C 330 "
           pdb=" N   PRO C 331 "
           pdb=" CA  PRO C 331 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  121.04   58.96     0      5.00e+00 4.00e-02 1.39e+02
  dihedral pdb=" CA  ASN C 191 "
           pdb=" C   ASN C 191 "
           pdb=" N   TRP C 192 "
           pdb=" CA  TRP C 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.94   22.06     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  MET C 193 "
           pdb=" C   MET C 193 "
           pdb=" N   LEU C 194 "
           pdb=" CA  LEU C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 742
       0.035 -    0.070: 239
       0.070 -    0.105: 67
       0.105 -    0.140: 34
       0.140 -    0.175: 4
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CG  LEU C 275 "
            pdb=" CB  LEU C 275 "
            pdb=" CD1 LEU C 275 "
            pdb=" CD2 LEU C 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" CB  ILE B  60 "
            pdb=" CA  ILE B  60 "
            pdb=" CG1 ILE B  60 "
            pdb=" CG2 ILE B  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CG  LEU B 214 "
            pdb=" CB  LEU B 214 "
            pdb=" CD1 LEU B 214 "
            pdb=" CD2 LEU B 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.17 2.00e-01 2.50e+01 6.83e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 1268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 181 "   -0.078 5.00e-02 4.00e+02   1.15e-01 2.12e+01
        pdb=" N   PRO C 182 "    0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO C 182 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO C 182 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 330 "   -0.059 5.00e-02 4.00e+02   9.09e-02 1.32e+01
        pdb=" N   PRO C 331 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO C 331 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C 331 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 241 "    0.057 5.00e-02 4.00e+02   8.63e-02 1.19e+01
        pdb=" N   PRO C 242 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO C 242 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C 242 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1265 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 81
        2.64 -     3.21: 6343
        3.21 -     3.77: 10772
        3.77 -     4.34: 14363
        4.34 -     4.90: 24114
  Nonbonded interactions: 55673
  Sorted by model distance:
  nonbonded pdb=" O   PRO C 206 "
            pdb=" OG1 THR C 216 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" OG1 THR C 344 "
            pdb=" O   LYS C 349 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   VAL C  52 "
            pdb=" OG1 THR C  57 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OD1 ASP C  40 "
            pdb=" N   LYS C  41 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR B 280 "
            pdb=" OD1 ASP B 458 "
     model   vdw
     2.214 3.040
  ... (remaining 55668 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   7475  Z= 0.128
  Angle     :  0.656  20.119  10107  Z= 0.353
  Chirality :  0.042   0.175   1086
  Planarity :  0.006   0.115   1268
  Dihedral  : 16.500  83.263   2789
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.99 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 23.01 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.29), residues: 877
  helix:  1.64 (0.32), residues: 277
  sheet:  0.64 (0.43), residues: 157
  loop : -1.17 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 416 
 TYR   0.014   0.001   TYR B  37 
 PHE   0.011   0.001   PHE C 391 
 TRP   0.049   0.002   TRP C  20 
 HIS   0.006   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7475)
  covalent geometry    : angle       0.65589 (10107)
  hydrogen bonds       : bond        0.12229 (  284)
  hydrogen bonds       : angle       5.46972 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 111
  average time/residue: 0.0701
  time to fit residues: 10.9177
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.178843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136348 restraints weight = 9729.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.134459 restraints weight = 7920.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.136571 restraints weight = 7676.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.136771 restraints weight = 5576.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137457 restraints weight = 5774.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7475  Z= 0.200
  Angle     :  0.608   9.533  10107  Z= 0.316
  Chirality :  0.043   0.151   1086
  Planarity :  0.006   0.084   1268
  Dihedral  :  6.330  63.752    984
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.79 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 21.24 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.28), residues: 877
  helix:  1.37 (0.31), residues: 282
  sheet:  0.42 (0.43), residues: 157
  loop : -1.13 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 416 
 TYR   0.010   0.001   TYR C 171 
 PHE   0.015   0.002   PHE C  45 
 TRP   0.030   0.002   TRP C  20 
 HIS   0.007   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 7475)
  covalent geometry    : angle       0.60769 (10107)
  hydrogen bonds       : bond        0.04441 (  284)
  hydrogen bonds       : angle       4.79268 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  280 TYR cc_start: 0.8261 (m-80) cc_final: 0.8016 (m-10)
REVERT: C  107 ASP cc_start: 0.7543 (t0) cc_final: 0.7189 (t0)
REVERT: C  138 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7595 (mp10)
REVERT: C  192 TRP cc_start: 0.6258 (p90) cc_final: 0.5939 (p90)
REVERT: C  193 MET cc_start: 0.5641 (mmt) cc_final: 0.5346 (ttp)
REVERT: C  225 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6440 (p90)
REVERT: C  276 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6524 (mmm-85)
  outliers start: 38
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0751
  time to fit residues: 13.4907
Evaluate side-chains
  127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 82 optimal weight:   20.0000
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.181792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139485 restraints weight = 9294.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.138476 restraints weight = 7451.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.140121 restraints weight = 7566.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.140775 restraints weight = 5288.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.141372 restraints weight = 5205.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7475  Z= 0.124
  Angle     :  0.549  10.320  10107  Z= 0.282
  Chirality :  0.042   0.138   1086
  Planarity :  0.005   0.074   1268
  Dihedral  :  6.052  63.742    984
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.99 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 22.63 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.28), residues: 877
  helix:  1.59 (0.31), residues: 282
  sheet:  0.40 (0.42), residues: 159
  loop : -1.11 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 276 
 TYR   0.007   0.001   TYR B 346 
 PHE   0.011   0.001   PHE C  60 
 TRP   0.032   0.002   TRP C  20 
 HIS   0.006   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7475)
  covalent geometry    : angle       0.54922 (10107)
  hydrogen bonds       : bond        0.03758 (  284)
  hydrogen bonds       : angle       4.51396 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.285 
Fit side-chains
REVERT: C  107 ASP cc_start: 0.7542 (t0) cc_final: 0.7297 (t0)
REVERT: C  138 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7846 (mp10)
REVERT: C  174 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7941 (p0)
REVERT: C  225 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6364 (p90)
REVERT: C  276 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.6440 (mmm-85)
  outliers start: 34
  outliers final: 21
  residues processed: 129
  average time/residue: 0.0731
  time to fit residues: 13.3023
Evaluate side-chains
  120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  384 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 ASN
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.137231 restraints weight = 9729.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.134266 restraints weight = 9282.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.135699 restraints weight = 11332.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.136616 restraints weight = 7387.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137201 restraints weight = 6421.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7475  Z= 0.200
  Angle     :  0.603   9.476  10107  Z= 0.313
  Chirality :  0.044   0.144   1086
  Planarity :  0.005   0.077   1268
  Dihedral  :  5.941  63.755    981
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.36 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 24.27 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.28), residues: 877
  helix:  1.36 (0.31), residues: 282
  sheet:  0.23 (0.43), residues: 157
  loop : -1.11 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 275 
 TYR   0.012   0.001   TYR B 280 
 PHE   0.016   0.001   PHE C  17 
 TRP   0.041   0.003   TRP C  20 
 HIS   0.005   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 7475)
  covalent geometry    : angle       0.60268 (10107)
  hydrogen bonds       : bond        0.04327 (  284)
  hydrogen bonds       : angle       4.69835 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   56 TYR cc_start: 0.9050 (t80) cc_final: 0.8793 (t80)
REVERT: C    1 MET cc_start: 0.7121 (tpp) cc_final: 0.6761 (ttp)
REVERT: C  107 ASP cc_start: 0.7692 (t0) cc_final: 0.7181 (t0)
REVERT: C  138 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7552 (mp10)
REVERT: C  174 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8053 (p0)
REVERT: C  225 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6383 (p90)
REVERT: C  276 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6470 (mmm-85)
  outliers start: 40
  outliers final: 32
  residues processed: 128
  average time/residue: 0.0690
  time to fit residues: 12.7926
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 98
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0020
   chunk 48 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 116 ASN
C 174 ASN
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.179140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.136634 restraints weight = 9565.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135780 restraints weight = 7630.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.136889 restraints weight = 8289.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.137872 restraints weight = 5949.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138073 restraints weight = 5812.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7475  Z= 0.156
  Angle     :  0.571   9.892  10107  Z= 0.295
  Chirality :  0.042   0.140   1086
  Planarity :  0.005   0.076   1268
  Dihedral  :  5.858  63.747    981
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 24.27 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.28), residues: 877
  helix:  1.47 (0.31), residues: 283
  sheet:  0.24 (0.42), residues: 157
  loop : -1.08 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 275 
 TYR   0.010   0.001   TYR C 213 
 PHE   0.011   0.001   PHE C  60 
 TRP   0.052   0.002   TRP C  20 
 HIS   0.005   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 7475)
  covalent geometry    : angle       0.57092 (10107)
  hydrogen bonds       : bond        0.03924 (  284)
  hydrogen bonds       : angle       4.56256 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 0.305 
Fit side-chains
REVERT: C  107 ASP cc_start: 0.7720 (t0) cc_final: 0.7191 (t0)
REVERT: C  138 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7559 (mp10)
REVERT: C  174 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7968 (p0)
REVERT: C  225 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6375 (p90)
REVERT: C  276 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.6493 (mmm-85)
  outliers start: 40
  outliers final: 29
  residues processed: 130
  average time/residue: 0.0634
  time to fit residues: 11.9038
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
C 174 ASN
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.176082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136205 restraints weight = 9737.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.132929 restraints weight = 10198.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.134609 restraints weight = 11637.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.135367 restraints weight = 7766.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135862 restraints weight = 6896.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7475  Z= 0.227
  Angle     :  0.637   9.428  10107  Z= 0.333
  Chirality :  0.045   0.166   1086
  Planarity :  0.005   0.076   1268
  Dihedral  :  6.136  63.757    981
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.82 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 24.27 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.29), residues: 877
  helix:  1.04 (0.31), residues: 295
  sheet: -0.16 (0.42), residues: 157
  loop : -1.08 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 275 
 TYR   0.010   0.001   TYR C 213 
 PHE   0.016   0.002   PHE C  17 
 TRP   0.065   0.003   TRP C  20 
 HIS   0.004   0.001   HIS C 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 7475)
  covalent geometry    : angle       0.63735 (10107)
  hydrogen bonds       : bond        0.04583 (  284)
  hydrogen bonds       : angle       4.84635 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B   56 TYR cc_start: 0.9065 (t80) cc_final: 0.8863 (t80)
REVERT: C    1 MET cc_start: 0.7098 (tpp) cc_final: 0.6549 (ttp)
REVERT: C  107 ASP cc_start: 0.7798 (t0) cc_final: 0.7308 (t0)
REVERT: C  138 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7510 (mp10)
REVERT: C  225 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6503 (p90)
REVERT: C  276 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6297 (mmm-85)
REVERT: C  388 ASP cc_start: 0.8683 (m-30) cc_final: 0.8303 (p0)
  outliers start: 50
  outliers final: 41
  residues processed: 137
  average time/residue: 0.0624
  time to fit residues: 12.5434
Evaluate side-chains
  138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 94
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  374 LEU
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  355 SER
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   chunk 63 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.181814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.141073 restraints weight = 9503.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.139959 restraints weight = 8238.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.141654 restraints weight = 8766.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.142284 restraints weight = 5974.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.143000 restraints weight = 5593.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7475  Z= 0.108
  Angle     :  0.556  10.464  10107  Z= 0.285
  Chirality :  0.042   0.163   1086
  Planarity :  0.005   0.073   1268
  Dihedral  :  5.663  63.738    981
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 26.55 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.29), residues: 877
  helix:  1.47 (0.31), residues: 289
  sheet:  0.11 (0.42), residues: 162
  loop : -1.02 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 276 
 TYR   0.017   0.001   TYR C 105 
 PHE   0.011   0.001   PHE C 391 
 TRP   0.059   0.002   TRP C  20 
 HIS   0.002   0.000   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7475)
  covalent geometry    : angle       0.55598 (10107)
  hydrogen bonds       : bond        0.03460 (  284)
  hydrogen bonds       : angle       4.47723 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.281 
Fit side-chains
REVERT: B  243 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7459 (mtt180)
REVERT: C    1 MET cc_start: 0.6809 (tpp) cc_final: 0.6454 (ttp)
REVERT: C  107 ASP cc_start: 0.7708 (t0) cc_final: 0.7410 (t0)
REVERT: C  138 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7721 (mp10)
REVERT: C  225 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6366 (p90)
REVERT: C  276 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8221 (tpt-90)
REVERT: C  318 ASN cc_start: 0.6559 (m-40) cc_final: 0.6296 (m-40)
REVERT: C  388 ASP cc_start: 0.8569 (m-30) cc_final: 0.8218 (p0)
REVERT: C  393 LEU cc_start: 0.8064 (tp) cc_final: 0.7715 (tp)
  outliers start: 33
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0719
  time to fit residues: 12.9129
Evaluate side-chains
  117 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.180713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.137286 restraints weight = 9702.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136510 restraints weight = 7094.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137614 restraints weight = 7542.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138617 restraints weight = 5563.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.139063 restraints weight = 5181.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7475  Z= 0.119
  Angle     :  0.580  11.005  10107  Z= 0.294
  Chirality :  0.043   0.192   1086
  Planarity :  0.005   0.072   1268
  Dihedral  :  5.580  63.740    981
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.56 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.55 %
    Favored  : 69.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.29), residues: 877
  helix:  1.51 (0.31), residues: 294
  sheet: -0.12 (0.40), residues: 182
  loop : -0.85 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 275 
 TYR   0.014   0.001   TYR C 105 
 PHE   0.011   0.001   PHE C 332 
 TRP   0.045   0.002   TRP C  20 
 HIS   0.003   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7475)
  covalent geometry    : angle       0.58014 (10107)
  hydrogen bonds       : bond        0.03493 (  284)
  hydrogen bonds       : angle       4.42072 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  243 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7504 (mtt180)
REVERT: C    1 MET cc_start: 0.6973 (tpp) cc_final: 0.6612 (ttp)
REVERT: C  107 ASP cc_start: 0.7749 (t0) cc_final: 0.7412 (t0)
REVERT: C  138 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7832 (mp10)
REVERT: C  223 PHE cc_start: 0.6432 (m-80) cc_final: 0.6138 (m-80)
REVERT: C  225 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6512 (p90)
REVERT: C  276 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7927 (tpt-90)
REVERT: C  318 ASN cc_start: 0.6890 (m-40) cc_final: 0.6558 (m-40)
REVERT: C  388 ASP cc_start: 0.8683 (m-30) cc_final: 0.8259 (p0)
REVERT: C  393 LEU cc_start: 0.8056 (tp) cc_final: 0.7775 (tp)
  outliers start: 34
  outliers final: 27
  residues processed: 121
  average time/residue: 0.0714
  time to fit residues: 12.4405
Evaluate side-chains
  124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  389 SER
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  355 SER
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 70 optimal weight:    0.1980
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.181881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139590 restraints weight = 9396.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138124 restraints weight = 7449.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.140295 restraints weight = 7358.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.140880 restraints weight = 5487.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.141486 restraints weight = 5277.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7475  Z= 0.121
  Angle     :  0.582  10.285  10107  Z= 0.295
  Chirality :  0.042   0.166   1086
  Planarity :  0.005   0.072   1268
  Dihedral  :  5.510  63.741    981
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.02 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 26.93 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.29), residues: 877
  helix:  1.53 (0.31), residues: 295
  sheet:  0.29 (0.42), residues: 161
  loop : -0.83 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  54 
 TYR   0.012   0.001   TYR C 105 
 PHE   0.011   0.001   PHE C 332 
 TRP   0.061   0.002   TRP C  20 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7475)
  covalent geometry    : angle       0.58200 (10107)
  hydrogen bonds       : bond        0.03459 (  284)
  hydrogen bonds       : angle       4.36387 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: B  243 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7526 (mtt180)
REVERT: C    1 MET cc_start: 0.6805 (tpp) cc_final: 0.6451 (ttp)
REVERT: C  107 ASP cc_start: 0.7717 (t0) cc_final: 0.7383 (t0)
REVERT: C  138 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7908 (mp10)
REVERT: C  192 TRP cc_start: 0.5447 (p-90) cc_final: 0.5246 (p90)
REVERT: C  223 PHE cc_start: 0.6426 (m-80) cc_final: 0.6134 (m-80)
REVERT: C  225 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6498 (p90)
REVERT: C  276 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7919 (tpt-90)
REVERT: C  318 ASN cc_start: 0.6744 (m-40) cc_final: 0.6430 (m-40)
REVERT: C  388 ASP cc_start: 0.8545 (m-30) cc_final: 0.8227 (p0)
REVERT: C  393 LEU cc_start: 0.8036 (tp) cc_final: 0.7815 (tp)
  outliers start: 33
  outliers final: 29
  residues processed: 120
  average time/residue: 0.0678
  time to fit residues: 11.7235
Evaluate side-chains
  124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  389 SER
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  355 SER
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.178961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.135105 restraints weight = 9559.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.134550 restraints weight = 7132.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.135562 restraints weight = 7580.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.136592 restraints weight = 5754.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136851 restraints weight = 5345.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7475  Z= 0.161
  Angle     :  0.630   9.712  10107  Z= 0.318
  Chirality :  0.044   0.191   1086
  Planarity :  0.005   0.072   1268
  Dihedral  :  5.700  63.747    981
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.02 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.93 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.29), residues: 877
  helix:  1.45 (0.31), residues: 295
  sheet:  0.33 (0.43), residues: 158
  loop : -0.85 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 275 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.012   0.001   PHE C  17 
 TRP   0.057   0.002   TRP C  20 
 HIS   0.003   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7475)
  covalent geometry    : angle       0.62959 (10107)
  hydrogen bonds       : bond        0.03805 (  284)
  hydrogen bonds       : angle       4.47690 (  840)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 0.293 
Fit side-chains
REVERT: B   74 MET cc_start: 0.8047 (ppp) cc_final: 0.7761 (ppp)
REVERT: B  243 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7597 (mtt180)
REVERT: C    1 MET cc_start: 0.7084 (tpp) cc_final: 0.6725 (ttp)
REVERT: C  107 ASP cc_start: 0.7798 (t0) cc_final: 0.7467 (t0)
REVERT: C  138 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7729 (mp10)
REVERT: C  192 TRP cc_start: 0.5241 (p-90) cc_final: 0.5015 (p90)
REVERT: C  223 PHE cc_start: 0.6654 (m-80) cc_final: 0.6329 (m-80)
REVERT: C  225 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6595 (p90)
REVERT: C  276 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7928 (tpt-90)
REVERT: C  388 ASP cc_start: 0.8707 (m-30) cc_final: 0.8301 (p0)
REVERT: C  393 LEU cc_start: 0.8101 (tp) cc_final: 0.7826 (tp)
  outliers start: 34
  outliers final: 29
  residues processed: 116
  average time/residue: 0.0649
  time to fit residues: 10.9774
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  389 SER
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  225 TYR
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  276 ARG
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  355 SER
Chi-restraints excluded: chain C residue  370 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0170
   chunk 17 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.184447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140419 restraints weight = 9544.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.140411 restraints weight = 7044.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.141637 restraints weight = 6935.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.142587 restraints weight = 5311.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.142795 restraints weight = 5106.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7475  Z= 0.108
  Angle     :  0.598  10.721  10107  Z= 0.300
  Chirality :  0.043   0.182   1086
  Planarity :  0.004   0.071   1268
  Dihedral  :  5.407  63.737    981
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.88 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.31 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.29), residues: 877
  helix:  1.57 (0.31), residues: 296
  sheet:  0.25 (0.42), residues: 165
  loop : -0.79 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 407 
 TYR   0.012   0.001   TYR C 105 
 PHE   0.011   0.001   PHE C 332 
 TRP   0.061   0.002   TRP C  20 
 HIS   0.002   0.000   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7475)
  covalent geometry    : angle       0.59768 (10107)
  hydrogen bonds       : bond        0.03125 (  284)
  hydrogen bonds       : angle       4.28162 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1084.03 seconds
wall clock time: 19 minutes 30.59 seconds (1170.59 seconds total)