Starting phenix.real_space_refine
on Thu Sep 18 13:32:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dpb_47101/09_2025/9dpb_47101.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9120 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     P      79      5.49       5
     Mg      4      5.21       5
     S      56      5.16       5
     Na      1      4.78       5
     C    5970      2.51       5
     N    1680      2.21       5
     O    2046      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9836
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 4100
          Classifications: {'peptide': 506}
          Link IDs: {'PTRANS': 29, 'TRANS': 476}
    Chain: "B"
      Number of atoms: 4092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 4092
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 29, 'TRANS': 475}
    Chain: "C"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1557
          Classifications: {'RNA': 73}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 11, 'rna3p': 61}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'APC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'APC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.68, per 1000 atoms: 0.27
  Number of scatterers: 9836
  At special positions: 0
  Unit cell: (85.6, 103.79, 141.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      56     16.00
     P      79     15.00
     Mg      4     11.99
     Na      1     11.00
     O    2046      8.00
     N    1680      7.00
     C    5970      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: 0.69
  Conformation dependent library (CDL) restraints added in 422.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      38.7% alpha, 24.1% beta
      26 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 90
    Processing helix  chain 'A' and resid 104 through 113
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 238 through 261
      removed outlier: 3.782A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 346 through 367
      removed outlier: 4.300A  pdb=" N   GLU A 352 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 410 through 415
      removed outlier: 4.466A  pdb=" N   GLU A 415 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 453 through 456
    Processing helix  chain 'A' and resid 504 through 521
    Processing helix  chain 'A' and resid 530 through 538
      removed outlier: 3.724A  pdb=" N   GLU A 538 " --> pdb=" O   CYS A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 559
    Processing helix  chain 'A' and resid 563 through 567
    Processing helix  chain 'B' and resid 73 through 90
      removed outlier: 3.533A  pdb=" N   ASN B  90 " --> pdb=" O   GLN B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 165 through 174
      removed outlier: 3.669A  pdb=" N   ASN B 174 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 229
    Processing helix  chain 'B' and resid 229 through 237
    Processing helix  chain 'B' and resid 238 through 261
      removed outlier: 3.614A  pdb=" N   GLN B 242 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 311
    Processing helix  chain 'B' and resid 348 through 367
      removed outlier: 4.435A  pdb=" N   GLU B 352 " --> pdb=" O   HIS B 348 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 405
    Processing helix  chain 'B' and resid 416 through 430
      removed outlier: 3.538A  pdb=" N   ARG B 420 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 452
    Processing helix  chain 'B' and resid 468 through 470
      No H-bonds generated for 'chain 'B' and resid 468 through 470'
    Processing helix  chain 'B' and resid 504 through 522
    Processing helix  chain 'B' and resid 530 through 539
    Processing helix  chain 'B' and resid 551 through 559
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137
      removed outlier: 5.862A  pdb=" N   ILE A 132 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ALA A 134 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
      removed outlier: 8.613A  pdb=" N   LYS A 153 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   ILE A 198 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   GLN A 155 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   MET A 157 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 8.983A  pdb=" N   GLU A 202 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 10.160A  pdb=" N   ASN A 159 " --> pdb=" O   GLU A 202 " (cutoff:3.500A)
      removed outlier: 12.610A  pdb=" N   THR A 204 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE A 198 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLY A 189 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASN A 187 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265
      removed outlier: 5.932A  pdb=" N   LEU A 264 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   ILE A 318 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A 495 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   GLU A 494 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A 490 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   CYS A 496 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   ARG A 392 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466
      removed outlier: 3.889A  pdb=" N   HIS A 465 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159
      removed outlier: 3.919A  pdb=" N   ALA B 134 " --> pdb=" O   ASP B 146 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   ILE B 132 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   GLY B 183 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ILE B 203 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   GLN B 185 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265
      removed outlier: 5.854A  pdb=" N   LEU B 264 " --> pdb=" O   TYR B 316 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   ILE B 318 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B 495 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLU B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   VAL B 490 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   GLU B 484 " --> pdb=" O   THR B 500 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ARG B 392 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265
      removed outlier: 5.854A  pdb=" N   LEU B 264 " --> pdb=" O   TYR B 316 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   ILE B 318 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B 495 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLU B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   VAL B 490 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   GLU B 484 " --> pdb=" O   THR B 500 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   HIS B 465 " --> pdb=" O   THR B 483 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 272
    Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 373

    388 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      108 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2116
        1.33 -     1.45: 2612
        1.45 -     1.58: 5230
        1.58 -     1.70: 151
        1.70 -     1.82: 100
  Bond restraints: 10209
  Sorted by residual:
  bond pdb=" C   PRO B 375 "
       pdb=" N   ASP B 376 "
    ideal  model  delta    sigma   weight residual
    1.332  1.207  0.125 1.40e-02 5.10e+03 7.99e+01
  bond pdb=" C   GLY B 405 "
       pdb=" N   MET B 406 "
    ideal  model  delta    sigma   weight residual
    1.330  1.407 -0.077 1.53e-02 4.27e+03 2.56e+01
  bond pdb=" C   THR B 191 "
       pdb=" N   LYS B 192 "
    ideal  model  delta    sigma   weight residual
    1.335  1.401 -0.066 1.31e-02 5.83e+03 2.56e+01
  bond pdb=" C   GLY A 405 "
       pdb=" N   MET A 406 "
    ideal  model  delta    sigma   weight residual
    1.329  1.398 -0.068 1.36e-02 5.41e+03 2.51e+01
  bond pdb=" C   LYS B 135 "
       pdb=" N   ARG B 136 "
    ideal  model  delta    sigma   weight residual
    1.330  1.396 -0.065 1.45e-02 4.76e+03 2.03e+01
  ... (remaining 10204 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.27: 14139
        5.27 -    10.54: 17
       10.54 -    15.81: 2
       15.81 -    21.08: 0
       21.08 -    26.35: 2
  Bond angle restraints: 14160
  Sorted by residual:
  angle pdb=" PB  APC B 602 "
        pdb=" O3B APC B 602 "
        pdb=" PG  APC B 602 "
      ideal   model   delta    sigma   weight residual
     106.84  133.19  -26.35 3.00e+00 1.11e-01 7.72e+01
  angle pdb=" PB  APC A 602 "
        pdb=" O3B APC A 602 "
        pdb=" PG  APC A 602 "
      ideal   model   delta    sigma   weight residual
     106.84  131.47  -24.63 3.00e+00 1.11e-01 6.74e+01
  angle pdb=" O   PRO B 375 "
        pdb=" C   PRO B 375 "
        pdb=" N   ASP B 376 "
      ideal   model   delta    sigma   weight residual
     122.38  115.08    7.30 1.39e+00 5.18e-01 2.76e+01
  angle pdb=" C5' APC B 602 "
        pdb=" O5' APC B 602 "
        pdb=" PA  APC B 602 "
      ideal   model   delta    sigma   weight residual
     106.85  122.55  -15.70 3.00e+00 1.11e-01 2.74e+01
  angle pdb=" C5' APC A 602 "
        pdb=" O5' APC A 602 "
        pdb=" PA  APC A 602 "
      ideal   model   delta    sigma   weight residual
     106.85  122.21  -15.36 3.00e+00 1.11e-01 2.62e+01
  ... (remaining 14155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.38: 5881
       32.38 -    64.76: 412
       64.76 -    97.14: 40
       97.14 -   129.52: 2
      129.52 -   161.90: 1
  Dihedral angle restraints: 6336
    sinusoidal: 3385
      harmonic: 2951
  Sorted by residual:
  dihedral pdb=" O4'   U C  20 "
           pdb=" C1'   U C  20 "
           pdb=" N1    U C  20 "
           pdb=" C2    U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   38.10  161.90     1      1.50e+01 4.44e-03 8.32e+01
  dihedral pdb=" CA  ILE A 462 "
           pdb=" C   ILE A 462 "
           pdb=" N   CYS A 463 "
           pdb=" CA  CYS A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  TYR B 499 "
           pdb=" C   TYR B 499 "
           pdb=" N   THR B 500 "
           pdb=" CA  THR B 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.70   23.30     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 6333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1316
       0.050 -    0.100: 228
       0.100 -    0.150: 44
       0.150 -    0.200: 8
       0.200 -    0.250: 2
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" CG  LEU B 329 "
            pdb=" CB  LEU B 329 "
            pdb=" CD1 LEU B 329 "
            pdb=" CD2 LEU B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CG  LEU A 444 "
            pdb=" CB  LEU A 444 "
            pdb=" CD1 LEU A 444 "
            pdb=" CD2 LEU A 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE B 462 "
            pdb=" N   ILE B 462 "
            pdb=" C   ILE B 462 "
            pdb=" CB  ILE B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.79e-01
  ... (remaining 1595 not shown)

  Planarity restraints: 1549
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 376 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.03e+00
        pdb=" C   ASP B 376 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASP B 376 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY B 377 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 388 "   -0.032 5.00e-02 4.00e+02   4.79e-02 3.67e+00
        pdb=" N   PRO A 389 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 468 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.18e+00
        pdb=" C   ILE B 468 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ILE B 468 "    0.012 2.00e-02 2.50e+03
        pdb=" N   MET B 469 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1546 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1668
        2.76 -     3.30: 9423
        3.30 -     3.83: 17982
        3.83 -     4.37: 21263
        4.37 -     4.90: 34339
  Nonbonded interactions: 84675
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 195 "
            pdb=" OE1 GLU B 195 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" N   GLU A 453 "
            pdb=" OE1 GLU A 453 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OD2 ASP B 222 "
            pdb=" OG1 THR B 225 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OE2 GLU A 494 "
            pdb="MG    MG A 603 "
     model   vdw
     2.258 2.170
  nonbonded pdb=" OH  TYR B 286 "
            pdb=" OD1 ASP B 291 "
     model   vdw
     2.279 3.040
  ... (remaining 84670 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 72 through 576 or resid 601 through 604))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.910
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
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      :  0.005   0.125  10209  Z= 0.318
  Angle     :  0.770  26.351  14160  Z= 0.437
  Chirality :  0.041   0.250   1598
  Planarity :  0.005   0.048   1549
  Dihedral  : 19.843 161.904   4438
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 22.19 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.27), residues: 1007
  helix:  0.88 (0.27), residues: 366
  sheet: -0.28 (0.36), residues: 211
  loop : -1.06 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 161 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.026   0.001   PHE B 340 
 TRP   0.015   0.003   TRP B 547 
 HIS   0.011   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (10209)
  covalent geometry    : angle       0.76951 (14160)
  hydrogen bonds       : bond        0.11241 (  431)
  hydrogen bonds       : angle       6.44685 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  469 MET cc_start: 0.8014 (mpt) cc_final: 0.7776 (mpt)
  outliers start: 13
  outliers final: 10
  residues processed: 87
  average time/residue: 0.6365
  time to fit residues: 59.1369
Evaluate side-chains
  71 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0370
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 229 GLN
A 288 ASN
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
B 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.116340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071382 restraints weight = 18465.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.71
r_work: 0.2931 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.0806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10209  Z= 0.126
  Angle     :  0.531   8.740  14160  Z= 0.267
  Chirality :  0.037   0.246   1598
  Planarity :  0.004   0.048   1549
  Dihedral  : 19.412 162.031   2350
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.29 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.27), residues: 1007
  helix:  1.32 (0.28), residues: 371
  sheet: -0.20 (0.37), residues: 211
  loop : -0.91 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 247 
 TYR   0.011   0.001   TYR A 499 
 PHE   0.028   0.001   PHE B 340 
 TRP   0.014   0.002   TRP B 547 
 HIS   0.003   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10209)
  covalent geometry    : angle       0.53101 (14160)
  hydrogen bonds       : bond        0.04408 (  431)
  hydrogen bonds       : angle       5.03052 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.8735 (tt0) cc_final: 0.8234 (mm-30)
REVERT: A  453 GLU cc_start: 0.7951 (mp0) cc_final: 0.7733 (mp0)
REVERT: A  469 MET cc_start: 0.8229 (mpt) cc_final: 0.8018 (mpt)
REVERT: A  499 TYR cc_start: 0.8234 (m-80) cc_final: 0.7974 (m-80)
REVERT: B  192 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8800 (tmmt)
REVERT: B  485 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8356 (ttt180)
  outliers start: 28
  outliers final: 9
  residues processed: 89
  average time/residue: 0.5942
  time to fit residues: 56.6147
Evaluate side-chains
  72 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  469 MET
Chi-restraints excluded: chain B residue  485 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 56 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0980
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** 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 = 0.3964 r_free = 0.3964 target = 0.117324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.072964 restraints weight = 18513.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.73
r_work: 0.2935 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10209  Z= 0.113
  Angle     :  0.518   8.302  14160  Z= 0.258
  Chirality :  0.036   0.147   1598
  Planarity :  0.004   0.047   1549
  Dihedral  : 19.192 162.244   2336
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.40 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 1007
  helix:  1.42 (0.27), residues: 370
  sheet: -0.16 (0.37), residues: 211
  loop : -0.92 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 161 
 TYR   0.013   0.001   TYR A 499 
 PHE   0.026   0.001   PHE B 340 
 TRP   0.013   0.002   TRP B 547 
 HIS   0.002   0.000   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10209)
  covalent geometry    : angle       0.51804 (14160)
  hydrogen bonds       : bond        0.04047 (  431)
  hydrogen bonds       : angle       4.74536 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8191 (m-30)
REVERT: A  301 GLU cc_start: 0.8745 (tt0) cc_final: 0.8235 (tp30)
REVERT: A  450 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8348 (mp0)
REVERT: A  453 GLU cc_start: 0.7916 (mp0) cc_final: 0.7514 (OUTLIER)
REVERT: A  499 TYR cc_start: 0.8156 (m-80) cc_final: 0.7897 (m-80)
REVERT: B  161 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8556 (mtm-85)
REVERT: B  162 ASN cc_start: 0.9082 (m110) cc_final: 0.8563 (m110)
REVERT: B  406 MET cc_start: 0.7421 (pp-130) cc_final: 0.6595 (pmm)
  outliers start: 28
  outliers final: 11
  residues processed: 91
  average time/residue: 0.5916
  time to fit residues: 57.9229
Evaluate side-chains
  74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.116227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.072554 restraints weight = 18653.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.57
r_work: 0.3007 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10209  Z= 0.186
  Angle     :  0.550   8.946  14160  Z= 0.275
  Chirality :  0.038   0.146   1598
  Planarity :  0.005   0.049   1549
  Dihedral  : 19.142 161.999   2336
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.74 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 1007
  helix:  1.39 (0.27), residues: 369
  sheet: -0.24 (0.37), residues: 214
  loop : -0.84 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.014   0.001   TYR A 499 
 PHE   0.031   0.002   PHE A 340 
 TRP   0.014   0.003   TRP B 547 
 HIS   0.004   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (10209)
  covalent geometry    : angle       0.54982 (14160)
  hydrogen bonds       : bond        0.04340 (  431)
  hydrogen bonds       : angle       4.74740 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.8697 (tt0) cc_final: 0.8267 (tp30)
REVERT: A  453 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7655 (mp0)
REVERT: A  499 TYR cc_start: 0.8189 (m-80) cc_final: 0.7882 (m-80)
REVERT: B  161 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8492 (mpp80)
REVERT: B  162 ASN cc_start: 0.9122 (m110) cc_final: 0.8644 (m110)
REVERT: B  212 MET cc_start: 0.8877 (ttp) cc_final: 0.8566 (ttm)
REVERT: B  406 MET cc_start: 0.7193 (pp-130) cc_final: 0.6556 (pmm)
  outliers start: 31
  outliers final: 12
  residues processed: 90
  average time/residue: 0.5160
  time to fit residues: 50.4363
Evaluate side-chains
  75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0070
   chunk 89 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** 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 = 0.4018 r_free = 0.4018 target = 0.117478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073671 restraints weight = 18480.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.59
r_work: 0.3018 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10209  Z= 0.107
  Angle     :  0.522  10.918  14160  Z= 0.257
  Chirality :  0.036   0.158   1598
  Planarity :  0.004   0.048   1549
  Dihedral  : 19.024 162.678   2336
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.18 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.27), residues: 1007
  helix:  1.47 (0.27), residues: 371
  sheet: -0.23 (0.37), residues: 214
  loop : -0.82 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.016   0.001   TYR A 499 
 PHE   0.025   0.001   PHE B 340 
 TRP   0.015   0.002   TRP B 547 
 HIS   0.004   0.000   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10209)
  covalent geometry    : angle       0.52165 (14160)
  hydrogen bonds       : bond        0.03904 (  431)
  hydrogen bonds       : angle       4.53019 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8248 (m-30)
REVERT: A  301 GLU cc_start: 0.8741 (tt0) cc_final: 0.8281 (tp30)
REVERT: A  450 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8323 (mp0)
REVERT: A  453 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7688 (mp0)
REVERT: A  499 TYR cc_start: 0.8165 (m-80) cc_final: 0.7867 (m-80)
REVERT: B  161 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8481 (mtm-85)
REVERT: B  162 ASN cc_start: 0.9212 (m110) cc_final: 0.8422 (m110)
REVERT: B  406 MET cc_start: 0.7142 (pp-130) cc_final: 0.6641 (pp-130)
  outliers start: 28
  outliers final: 9
  residues processed: 86
  average time/residue: 0.5703
  time to fit residues: 52.9170
Evaluate side-chains
  75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 465 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.113874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.069999 restraints weight = 18789.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.56
r_work: 0.2955 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074  10209  Z= 0.330
  Angle     :  0.635  12.250  14160  Z= 0.321
  Chirality :  0.042   0.174   1598
  Planarity :  0.005   0.050   1549
  Dihedral  : 19.106 162.079   2333
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.85 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.27), residues: 1007
  helix:  1.16 (0.27), residues: 370
  sheet: -0.54 (0.36), residues: 222
  loop : -0.85 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 553 
 TYR   0.016   0.002   TYR A 499 
 PHE   0.035   0.003   PHE A 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.005   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00787 (10209)
  covalent geometry    : angle       0.63484 (14160)
  hydrogen bonds       : bond        0.04991 (  431)
  hydrogen bonds       : angle       4.90017 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.8705 (tt0) cc_final: 0.8264 (tp30)
REVERT: A  450 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8297 (mp0)
REVERT: A  453 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7689 (OUTLIER)
REVERT: A  469 MET cc_start: 0.7302 (mpp) cc_final: 0.6994 (mpt)
REVERT: B  162 ASN cc_start: 0.9156 (m110) cc_final: 0.8769 (m110)
REVERT: B  406 MET cc_start: 0.7083 (pp-130) cc_final: 0.6641 (pp-130)
REVERT: B  499 TYR cc_start: 0.8535 (m-10) cc_final: 0.8224 (m-80)
REVERT: B  601 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5815 (mttm)
  outliers start: 29
  outliers final: 14
  residues processed: 87
  average time/residue: 0.5892
  time to fit residues: 54.9896
Evaluate side-chains
  78 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  601 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 98 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.115948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.072011 restraints weight = 18456.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.57
r_work: 0.2986 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10209  Z= 0.130
  Angle     :  0.553  13.347  14160  Z= 0.272
  Chirality :  0.037   0.158   1598
  Planarity :  0.004   0.050   1549
  Dihedral  : 19.005 163.749   2333
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.96 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.27), residues: 1007
  helix:  1.33 (0.27), residues: 370
  sheet: -0.36 (0.36), residues: 214
  loop : -0.80 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 485 
 TYR   0.011   0.001   TYR A 316 
 PHE   0.028   0.001   PHE B 340 
 TRP   0.014   0.003   TRP B 547 
 HIS   0.010   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10209)
  covalent geometry    : angle       0.55332 (14160)
  hydrogen bonds       : bond        0.04095 (  431)
  hydrogen bonds       : angle       4.63306 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8218 (m-30)
REVERT: A  301 GLU cc_start: 0.8718 (tt0) cc_final: 0.8183 (tp30)
REVERT: A  450 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8228 (mp0)
REVERT: A  453 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7782 (mp0)
REVERT: A  469 MET cc_start: 0.7316 (mpp) cc_final: 0.6988 (mpt)
REVERT: B  161 ARG cc_start: 0.8780 (mpp80) cc_final: 0.8434 (mtm-85)
REVERT: B  162 ASN cc_start: 0.9132 (m-40) cc_final: 0.8604 (m110)
REVERT: B  406 MET cc_start: 0.7119 (pp-130) cc_final: 0.6590 (pp-130)
REVERT: B  499 TYR cc_start: 0.8486 (m-10) cc_final: 0.8189 (m-80)
REVERT: B  601 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5418 (mttm)
  outliers start: 19
  outliers final: 10
  residues processed: 79
  average time/residue: 0.6500
  time to fit residues: 55.0965
Evaluate side-chains
  75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  601 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 90 optimal weight:    8.9990
   chunk 105 optimal weight:   30.0000
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.115852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.072185 restraints weight = 18400.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.55
r_work: 0.2981 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10209  Z= 0.148
  Angle     :  0.568  13.441  14160  Z= 0.278
  Chirality :  0.037   0.151   1598
  Planarity :  0.004   0.052   1549
  Dihedral  : 18.948 163.312   2333
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 23.19 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.27), residues: 1007
  helix:  1.41 (0.27), residues: 368
  sheet: -0.39 (0.36), residues: 214
  loop : -0.82 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.017   0.001   TYR A 499 
 PHE   0.030   0.002   PHE A 340 
 TRP   0.015   0.003   TRP B 547 
 HIS   0.008   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10209)
  covalent geometry    : angle       0.56803 (14160)
  hydrogen bonds       : bond        0.04142 (  431)
  hydrogen bonds       : angle       4.60316 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.8719 (tt0) cc_final: 0.8284 (tp30)
REVERT: A  450 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8254 (mp0)
REVERT: A  453 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7776 (mp0)
REVERT: A  469 MET cc_start: 0.7317 (mpp) cc_final: 0.7046 (mpt)
REVERT: B  161 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8323 (mtm-85)
REVERT: B  162 ASN cc_start: 0.9267 (m-40) cc_final: 0.8522 (m110)
REVERT: B  406 MET cc_start: 0.7224 (pp-130) cc_final: 0.6651 (pp-130)
REVERT: B  499 TYR cc_start: 0.8455 (m-10) cc_final: 0.8187 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 74
  average time/residue: 0.6789
  time to fit residues: 53.8597
Evaluate side-chains
  74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0020
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.2980
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** 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 = 0.4007 r_free = 0.4007 target = 0.116646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.072703 restraints weight = 18505.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.58
r_work: 0.3004 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10209  Z= 0.125
  Angle     :  0.557  13.490  14160  Z= 0.271
  Chirality :  0.037   0.146   1598
  Planarity :  0.004   0.052   1549
  Dihedral  : 18.871 163.406   2333
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 23.30 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.27), residues: 1007
  helix:  1.49 (0.27), residues: 368
  sheet: -0.40 (0.36), residues: 216
  loop : -0.81 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 161 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.027   0.001   PHE B 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.011   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10209)
  covalent geometry    : angle       0.55737 (14160)
  hydrogen bonds       : bond        0.03982 (  431)
  hydrogen bonds       : angle       4.51346 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8212 (m-30)
REVERT: A  292 MET cc_start: 0.8363 (ptt) cc_final: 0.8116 (pmt)
REVERT: A  301 GLU cc_start: 0.8710 (tt0) cc_final: 0.8266 (tp30)
REVERT: A  450 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8293 (mp0)
REVERT: A  453 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7810 (mp0)
REVERT: A  469 MET cc_start: 0.7310 (mpp) cc_final: 0.7050 (mpt)
REVERT: B  161 ARG cc_start: 0.8779 (mpp80) cc_final: 0.8258 (mtm-85)
REVERT: B  162 ASN cc_start: 0.9243 (m-40) cc_final: 0.8475 (m110)
REVERT: B  406 MET cc_start: 0.7182 (pp-130) cc_final: 0.6568 (pp-130)
REVERT: B  499 TYR cc_start: 0.8366 (m-10) cc_final: 0.8097 (m-80)
  outliers start: 18
  outliers final: 8
  residues processed: 76
  average time/residue: 0.6787
  time to fit residues: 55.3287
Evaluate side-chains
  72 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0970
   chunk 66 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0060
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.118401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.075114 restraints weight = 18382.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.57
r_work: 0.3035 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10209  Z= 0.104
  Angle     :  0.555  13.490  14160  Z= 0.269
  Chirality :  0.037   0.312   1598
  Planarity :  0.004   0.053   1549
  Dihedral  : 18.779 163.063   2333
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.75 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.27), residues: 1007
  helix:  1.65 (0.27), residues: 368
  sheet: -0.21 (0.37), residues: 210
  loop : -0.83 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 161 
 TYR   0.019   0.001   TYR A 499 
 PHE   0.025   0.001   PHE A 340 
 TRP   0.020   0.003   TRP A 475 
 HIS   0.013   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10209)
  covalent geometry    : angle       0.55479 (14160)
  hydrogen bonds       : bond        0.03858 (  431)
  hydrogen bonds       : angle       4.40638 ( 1227)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8239 (m-30)
REVERT: A  301 GLU cc_start: 0.8679 (tt0) cc_final: 0.8269 (tp30)
REVERT: A  402 LYS cc_start: 0.9290 (mttp) cc_final: 0.8974 (mtmm)
REVERT: A  450 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8309 (mp0)
REVERT: A  453 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7886 (mp0)
REVERT: A  469 MET cc_start: 0.7181 (mpp) cc_final: 0.6907 (mpt)
REVERT: B  161 ARG cc_start: 0.8786 (mpp80) cc_final: 0.8390 (mpp80)
REVERT: B  162 ASN cc_start: 0.9248 (m-40) cc_final: 0.8916 (m110)
REVERT: B  406 MET cc_start: 0.7102 (pp-130) cc_final: 0.6453 (pp-130)
REVERT: B  499 TYR cc_start: 0.8311 (m-10) cc_final: 0.8109 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 79
  average time/residue: 0.6594
  time to fit residues: 56.0326
Evaluate side-chains
  76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    0.2980
   chunk 27 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0970
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.118513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.075007 restraints weight = 18443.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.59
r_work: 0.3031 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10209  Z= 0.110
  Angle     :  0.574  13.387  14160  Z= 0.276
  Chirality :  0.037   0.332   1598
  Planarity :  0.004   0.052   1549
  Dihedral  : 18.742 162.599   2333
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 23.97 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.27), residues: 1007
  helix:  1.67 (0.27), residues: 368
  sheet: -0.18 (0.37), residues: 210
  loop : -0.81 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.026   0.001   PHE A 340 
 TRP   0.024   0.003   TRP A 475 
 HIS   0.010   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10209)
  covalent geometry    : angle       0.57396 (14160)
  hydrogen bonds       : bond        0.03888 (  431)
  hydrogen bonds       : angle       4.38073 ( 1227)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3117.94 seconds
wall clock time: 53 minutes 52.51 seconds (3232.51 seconds total)