Starting phenix.real_space_refine
on Fri Aug 22 20:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzb_20533/08_2025/6pzb_20533_neut.cif"
  }
  resolution = 4.55
  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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    4834      2.51       5
     N    1468      2.21       5
     O    1440      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 7747
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "G"
      Number of atoms: 7747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1357, 7747
          Classifications: {'peptide': 1357}
          Incomplete info: {'truncation_to_alanine': 915}
          Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 1313}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 3073
          Unresolved non-hydrogen angles: 3921
          Unresolved non-hydrogen dihedrals: 2428
          Unresolved non-hydrogen chiralities: 416
          Planarities with less than four sites: {'GLU:plan': 51, 'ASP:plan': 46, 'GLN:plan1': 52, 'ASN:plan1': 36, 'HIS:plan': 13, 'PHE:plan': 46, 'ARG:plan': 58, 'TYR:plan': 12, 'TRP:plan': 7}
          Unresolved non-hydrogen planarities: 1436
  Time building chain proxies: 2.11, per 1000 atoms: 0.27
  Number of scatterers: 7747
  At special positions: 0
  Unit cell: (113.212, 96.778, 142.428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O    1440      8.00
     N    1468      7.00
     C    4834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS G   6 " - pdb=" SG  CYS G  26 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 315.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2568

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      68.9% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'G' and resid 26 through 52
      removed outlier: 3.662A  pdb=" N   ALA G  30 " --> pdb=" O   CYS G  26 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL G  34 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      Proline residue:  G  35  - end of helix
      Proline residue:  G  45  - end of helix
    Processing helix  chain 'G' and resid 71 through 98
      removed outlier: 4.272A  pdb=" N   VAL G  98 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 108 through 130
      removed outlier: 3.755A  pdb=" N   MET G 112 " --> pdb=" O   MET G 108 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER G 130 " --> pdb=" O   ASN G 126 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 132 through 135
    Processing helix  chain 'G' and resid 136 through 160
    Processing helix  chain 'G' and resid 166 through 194
      removed outlier: 4.071A  pdb=" N   CYS G 170 " --> pdb=" O   GLN G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 208 through 213
    Processing helix  chain 'G' and resid 223 through 230
    Processing helix  chain 'G' and resid 231 through 241
      removed outlier: 4.321A  pdb=" N   ALA G 235 " --> pdb=" O   TRP G 231 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE G 236 " --> pdb=" O   TRP G 232 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 254 through 257
    Processing helix  chain 'G' and resid 258 through 276
    Processing helix  chain 'G' and resid 284 through 329
      removed outlier: 5.731A  pdb=" N   ARG G 297 " --> pdb=" O   HIS G 293 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ARG G 298 " --> pdb=" O   ALA G 294 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLY G 316 " --> pdb=" O   LEU G 312 " (cutoff:3.500A)
      Proline residue:  G 317  - end of helix
    Processing helix  chain 'G' and resid 347 through 352
    Processing helix  chain 'G' and resid 355 through 400
      removed outlier: 4.588A  pdb=" N   THR G 371 " --> pdb=" O   LEU G 367 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   GLN G 374 " --> pdb=" O   ARG G 370 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 413 through 435
    Processing helix  chain 'G' and resid 436 through 457
      Proline residue:  G 442  - end of helix
    Processing helix  chain 'G' and resid 466 through 469
    Processing helix  chain 'G' and resid 470 through 505
      removed outlier: 3.507A  pdb=" N   GLN G 474 " --> pdb=" O   LEU G 470 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU G 494 " --> pdb=" O   GLU G 490 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY G 505 " --> pdb=" O   GLU G 501 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 505 through 512
    Processing helix  chain 'G' and resid 515 through 548
      removed outlier: 4.080A  pdb=" N   SER G 543 " --> pdb=" O   TYR G 539 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE G 544 " --> pdb=" O   THR G 540 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 549 through 564
      removed outlier: 3.515A  pdb=" N   ALA G 553 " --> pdb=" O   ALA G 549 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 577 through 615
      Proline residue:  G 589  - end of helix
      removed outlier: 4.295A  pdb=" N   LEU G 592 " --> pdb=" O   THR G 588 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER G 615 " --> pdb=" O   SER G 611 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 718 through 727
    Processing helix  chain 'G' and resid 785 through 790
    Processing helix  chain 'G' and resid 795 through 806
      removed outlier: 3.530A  pdb=" N   TYR G 799 " --> pdb=" O   ASN G 795 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 808 through 815
    Processing helix  chain 'G' and resid 831 through 846
      removed outlier: 4.056A  pdb=" N   GLN G 846 " --> pdb=" O   ARG G 842 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 862 through 881
      removed outlier: 3.755A  pdb=" N   LYS G 881 " --> pdb=" O   LEU G 877 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 913 through 918
      removed outlier: 3.885A  pdb=" N   PHE G 917 " --> pdb=" O   THR G 913 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 922 through 927
      removed outlier: 3.842A  pdb=" N   GLU G 926 " --> pdb=" O   CYS G 922 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 996 through 1009
      removed outlier: 3.513A  pdb=" N   GLY G1009 " --> pdb=" O   LEU G1005 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1009 through 1041
      removed outlier: 4.376A  pdb=" N   LEU G1015 " --> pdb=" O   LEU G1011 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1070 through 1107
    Processing helix  chain 'G' and resid 1109 through 1116
      removed outlier: 3.974A  pdb=" N   PHE G1113 " --> pdb=" O   PRO G1109 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1117 through 1135
      removed outlier: 3.796A  pdb=" N   ILE G1121 " --> pdb=" O   PRO G1117 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ASP G1128 " --> pdb=" O   ARG G1124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1135 through 1161
      removed outlier: 3.707A  pdb=" N   THR G1139 " --> pdb=" O   HIS G1135 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU G1148 " --> pdb=" O   SER G1144 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1164 through 1210
      Proline residue:  G1170  - end of helix
      removed outlier: 4.003A  pdb=" N   ASP G1188 " --> pdb=" O   VAL G1184 " (cutoff:3.500A)
      Proline residue:  G1199  - end of helix
      removed outlier: 3.614A  pdb=" N   GLY G1210 " --> pdb=" O   GLU G1206 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1210 through 1218
      removed outlier: 3.678A  pdb=" N   ILE G1214 " --> pdb=" O   GLY G1210 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1219 through 1273
      removed outlier: 4.025A  pdb=" N   PHE G1223 " --> pdb=" O   TYR G1219 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA G1237 " --> pdb=" O   SER G1233 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   HIS G1273 " --> pdb=" O   SER G1269 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1278 through 1321
      removed outlier: 3.625A  pdb=" N   SER G1292 " --> pdb=" O   ALA G1288 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASN G1293 " --> pdb=" O   LEU G1289 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ASN G1296 " --> pdb=" O   SER G1292 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA G1311 " --> pdb=" O   ILE G1307 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL G1312 " --> pdb=" O   GLN G1308 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG G1314 " --> pdb=" O   GLY G1310 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR G1321 " --> pdb=" O   ALA G1317 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1385 through 1392
    Processing helix  chain 'G' and resid 1414 through 1421
      removed outlier: 3.855A  pdb=" N   ARG G1421 " --> pdb=" O   THR G1417 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1435 through 1441
    Processing helix  chain 'G' and resid 1447 through 1458
      removed outlier: 3.668A  pdb=" N   LEU G1451 " --> pdb=" O   SER G1447 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1460 through 1465
    Processing helix  chain 'G' and resid 1484 through 1498
      removed outlier: 4.240A  pdb=" N   GLN G1488 " --> pdb=" O   GLN G1484 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1512 through 1530
    Processing helix  chain 'G' and resid 1539 through 1543
    Processing helix  chain 'G' and resid 1564 through 1570
      removed outlier: 3.832A  pdb=" N   SER G1568 " --> pdb=" O   GLU G1564 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1571 through 1576
    Processing sheet with id=AA1, first strand: chain 'G' and resid 701 through 703
    Processing sheet with id=AA2, first strand: chain 'G' and resid 696 through 697
    Processing sheet with id=AA3, first strand: chain 'G' and resid 850 through 854
      removed outlier: 6.514A  pdb=" N   VAL G 851 " --> pdb=" O   VAL G 885 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   VAL G 887 " --> pdb=" O   VAL G 851 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU G 853 " --> pdb=" O   VAL G 887 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   ILE G 901 " --> pdb=" O   LEU G 708 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   MET G 710 " --> pdb=" O   ILE G 901 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   MET G 903 " --> pdb=" O   MET G 710 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL G 712 " --> pdb=" O   MET G 903 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA G 902 " --> pdb=" O   GLN G 909 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 1347 through 1348
    Processing sheet with id=AA5, first strand: chain 'G' and resid 1352 through 1353
      removed outlier: 3.805A  pdb=" N   ASP G1397 " --> pdb=" O   ARG G1353 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 1549 through 1551

    693 hydrogen bonds defined for protein.
    2037 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: 1.04

  Time building geometry restraints manager: 0.80 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: 2166
        1.33 -     1.45: 1399
        1.45 -     1.56: 4312
        1.56 -     1.68: 0
        1.68 -     1.80: 6
  Bond restraints: 7883
  Sorted by residual:
  bond pdb=" CB  TRP G  75 "
       pdb=" CG  TRP G  75 "
    ideal  model  delta    sigma   weight residual
    1.498  1.404  0.094 3.10e-02 1.04e+03 9.26e+00
  bond pdb=" CB  TRP G 778 "
       pdb=" CG  TRP G 778 "
    ideal  model  delta    sigma   weight residual
    1.498  1.414  0.084 3.10e-02 1.04e+03 7.33e+00
  bond pdb=" CB  TRP G 231 "
       pdb=" CG  TRP G 231 "
    ideal  model  delta    sigma   weight residual
    1.498  1.421  0.077 3.10e-02 1.04e+03 6.14e+00
  bond pdb=" CA  TYR G1287 "
       pdb=" C   TYR G1287 "
    ideal  model  delta    sigma   weight residual
    1.522  1.488  0.033 1.37e-02 5.33e+03 5.97e+00
  bond pdb=" CB  VAL G 596 "
       pdb=" CG2 VAL G 596 "
    ideal  model  delta    sigma   weight residual
    1.521  1.441  0.080 3.30e-02 9.18e+02 5.82e+00
  ... (remaining 7878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 10350
        2.53 -     5.05: 506
        5.05 -     7.58: 51
        7.58 -    10.11: 17
       10.11 -    12.64: 9
  Bond angle restraints: 10933
  Sorted by residual:
  angle pdb=" N   LEU G 104 "
        pdb=" CA  LEU G 104 "
        pdb=" C   LEU G 104 "
      ideal   model   delta    sigma   weight residual
     111.54  120.73   -9.19 1.36e+00 5.41e-01 4.57e+01
  angle pdb=" N   GLY G  97 "
        pdb=" CA  GLY G  97 "
        pdb=" C   GLY G  97 "
      ideal   model   delta    sigma   weight residual
     113.86  123.25   -9.39 1.50e+00 4.44e-01 3.92e+01
  angle pdb=" N   GLY G 316 "
        pdb=" CA  GLY G 316 "
        pdb=" C   GLY G 316 "
      ideal   model   delta    sigma   weight residual
     112.34  124.86  -12.52 2.04e+00 2.40e-01 3.77e+01
  angle pdb=" C   ARG G 102 "
        pdb=" N   HIS G 103 "
        pdb=" CA  HIS G 103 "
      ideal   model   delta    sigma   weight residual
     121.70  132.56  -10.86 1.80e+00 3.09e-01 3.64e+01
  angle pdb=" CA  ARG G 370 "
        pdb=" CB  ARG G 370 "
        pdb=" CG  ARG G 370 "
      ideal   model   delta    sigma   weight residual
     114.10  102.33   11.77 2.00e+00 2.50e-01 3.46e+01
  ... (remaining 10928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.87: 4349
       13.87 -    27.74: 130
       27.74 -    41.61: 19
       41.61 -    55.48: 4
       55.48 -    69.35: 2
  Dihedral angle restraints: 4504
    sinusoidal: 568
      harmonic: 3936
  Sorted by residual:
  dihedral pdb=" CA  ILE G 996 "
           pdb=" C   ILE G 996 "
           pdb=" N   PRO G 997 "
           pdb=" CA  PRO G 997 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.28  -42.72     0      5.00e+00 4.00e-02 7.30e+01
  dihedral pdb=" CB  CYS G   6 "
           pdb=" SG  CYS G   6 "
           pdb=" SG  CYS G  26 "
           pdb=" CB  CYS G  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.56  -50.56     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CA  ARG G 102 "
           pdb=" C   ARG G 102 "
           pdb=" N   HIS G 103 "
           pdb=" CA  HIS G 103 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -28.18   28.18     0      5.00e+00 4.00e-02 3.18e+01
  ... (remaining 4501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1114
       0.074 -    0.149: 203
       0.149 -    0.223: 24
       0.223 -    0.297: 8
       0.297 -    0.372: 2
  Chirality restraints: 1351
  Sorted by residual:
  chirality pdb=" CA  PHE G  79 "
            pdb=" N   PHE G  79 "
            pdb=" C   PHE G  79 "
            pdb=" CB  PHE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  ARG G 370 "
            pdb=" N   ARG G 370 "
            pdb=" C   ARG G 370 "
            pdb=" CB  ARG G 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  PHE G 295 "
            pdb=" N   PHE G 295 "
            pdb=" C   PHE G 295 "
            pdb=" CB  PHE G 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1348 not shown)

  Planarity restraints: 1508
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G1286 "    0.046 2.00e-02 2.50e+03   9.17e-02 8.41e+01
        pdb=" C   THR G1286 "   -0.159 2.00e-02 2.50e+03
        pdb=" O   THR G1286 "    0.058 2.00e-02 2.50e+03
        pdb=" N   TYR G1287 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G 297 "   -0.041 2.00e-02 2.50e+03   8.10e-02 6.56e+01
        pdb=" C   ARG G 297 "    0.140 2.00e-02 2.50e+03
        pdb=" O   ARG G 297 "   -0.052 2.00e-02 2.50e+03
        pdb=" N   ARG G 298 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G1283 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.19e+01
        pdb=" C   LEU G1283 "    0.098 2.00e-02 2.50e+03
        pdb=" O   LEU G1283 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLY G1284 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 1505 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1763
        2.76 -     3.30: 7690
        3.30 -     3.83: 12664
        3.83 -     4.37: 12260
        4.37 -     4.90: 20825
  Nonbonded interactions: 55202
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G 371 "
            pdb=" OH  TYR G1254 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ALA G 484 "
            pdb=" OG1 THR G 488 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLU G 791 "
            pdb=" OH  TYR G1219 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   TRP G 778 "
            pdb=" NH2 ARG G 842 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   THR G 789 "
            pdb=" OG  SER G 792 "
     model   vdw
     2.354 3.040
  ... (remaining 55197 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.060
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
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      :  0.009   0.098   7884  Z= 0.475
  Angle     :  1.244  12.636  10935  Z= 0.756
  Chirality :  0.061   0.372   1351
  Planarity :  0.012   0.092   1508
  Dihedral  :  8.371  69.349   1933
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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: -3.87 (0.18), residues: 1333
  helix: -1.89 (0.13), residues: 886
  sheet: -3.83 (0.50), residues: 61
  loop : -3.62 (0.26), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG G  16 
 TYR   0.039   0.005   TYR G1219 
 PHE   0.046   0.004   PHE G 221 
 TRP   0.054   0.007   TRP G1297 
 HIS   0.018   0.004   HIS G 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00890 ( 7883)
  covalent geometry    : angle       1.24254 (10933)
  SS BOND              : bond        0.00386 (    1)
  SS BOND              : angle       5.08008 (    2)
  hydrogen bonds       : bond        0.13638 (  693)
  hydrogen bonds       : angle       6.39373 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.255 
Fit side-chains
REVERT: G   28 VAL cc_start: 0.9010 (m) cc_final: 0.8749 (p)
REVERT: G  217 PHE cc_start: 0.8479 (t80) cc_final: 0.7944 (t80)
REVERT: G  264 GLN cc_start: 0.9479 (mm110) cc_final: 0.9162 (mm110)
REVERT: G  394 LYS cc_start: 0.9805 (tptm) cc_final: 0.9570 (tppp)
REVERT: G  433 PHE cc_start: 0.9060 (m-10) cc_final: 0.8512 (m-80)
REVERT: G  485 GLN cc_start: 0.9564 (tt0) cc_final: 0.9328 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0536
  time to fit residues: 6.9525
Evaluate side-chains
  61 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:   40.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:   50.0000
   chunk 91 optimal weight:   50.0000
   chunk 55 optimal weight:   20.0000
   overall best weight:    9.3992

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

Flipped N/Q/H residues before XYZ refinement:
G  32 ASN
G  71 HIS
** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 293 HIS
G 584 HIS
** G1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.069046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.056124 restraints weight = 53428.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.057198 restraints weight = 37983.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.057937 restraints weight = 28965.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.058497 restraints weight = 23537.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058893 restraints weight = 19913.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7884  Z= 0.260
  Angle     :  0.689   8.216  10935  Z= 0.400
  Chirality :  0.043   0.182   1351
  Planarity :  0.006   0.053   1508
  Dihedral  :  5.123  40.350   1381
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.18 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    Twisted General : 0.08 %

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: -1.04 (0.22), residues: 1333
  helix:  0.49 (0.17), residues: 887
  sheet: -3.94 (0.51), residues: 54
  loop : -2.93 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 168 
 TYR   0.024   0.003   TYR G 124 
 PHE   0.018   0.002   PHE G1182 
 TRP   0.027   0.003   TRP G 288 
 HIS   0.009   0.002   HIS G  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 7883)
  covalent geometry    : angle       0.68791 (10933)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       2.38508 (    2)
  hydrogen bonds       : bond        0.05322 (  693)
  hydrogen bonds       : angle       4.88056 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: G  217 PHE cc_start: 0.8353 (t80) cc_final: 0.7940 (t80)
REVERT: G  263 TYR cc_start: 0.8681 (t80) cc_final: 0.8237 (t80)
REVERT: G  394 LYS cc_start: 0.9815 (tptm) cc_final: 0.9305 (tppp)
REVERT: G  433 PHE cc_start: 0.9181 (m-10) cc_final: 0.8730 (m-80)
REVERT: G  485 GLN cc_start: 0.9574 (tt0) cc_final: 0.9306 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0481
  time to fit residues: 5.2358
Evaluate side-chains
  57 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:   50.0000
   chunk 54 optimal weight:    6.9990
   chunk 78 optimal weight:   30.0000
   chunk 19 optimal weight:   40.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
G  71 HIS
G 125 HIS
G 262 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.059414 restraints weight = 56384.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060331 restraints weight = 40334.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061048 restraints weight = 30866.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061486 restraints weight = 25020.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.061869 restraints weight = 21436.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7884  Z= 0.161
  Angle     :  0.560   7.138  10935  Z= 0.314
  Chirality :  0.041   0.152   1351
  Planarity :  0.004   0.045   1508
  Dihedral  :  4.456  33.674   1381
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  0.19 (0.23), residues: 1333
  helix:  1.46 (0.17), residues: 903
  sheet: -3.79 (0.56), residues: 53
  loop : -2.67 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 798 
 TYR   0.018   0.002   TYR G 124 
 PHE   0.019   0.001   PHE G1204 
 TRP   0.017   0.002   TRP G 288 
 HIS   0.008   0.001   HIS G  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7883)
  covalent geometry    : angle       0.55927 (10933)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       1.38247 (    2)
  hydrogen bonds       : bond        0.04419 (  693)
  hydrogen bonds       : angle       4.21021 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.307 
Fit side-chains
REVERT: G  263 TYR cc_start: 0.8470 (t80) cc_final: 0.7913 (t80)
REVERT: G  264 GLN cc_start: 0.9150 (mp10) cc_final: 0.8912 (mp10)
REVERT: G  394 LYS cc_start: 0.9787 (tptm) cc_final: 0.9288 (tppp)
REVERT: G  433 PHE cc_start: 0.8955 (m-10) cc_final: 0.8646 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0470
  time to fit residues: 5.1594
Evaluate side-chains
  56 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 83 optimal weight:   30.0000
   chunk 66 optimal weight:   40.0000
   chunk 112 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 98 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   overall best weight:    4.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059330 restraints weight = 57184.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060249 restraints weight = 41401.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.060941 restraints weight = 32018.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.061437 restraints weight = 25997.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061787 restraints weight = 22074.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7884  Z= 0.146
  Angle     :  0.532   6.867  10935  Z= 0.294
  Chirality :  0.041   0.133   1351
  Planarity :  0.004   0.045   1508
  Dihedral  :  4.221  34.617   1381
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  0.76 (0.24), residues: 1333
  helix:  1.92 (0.17), residues: 905
  sheet: -3.70 (0.58), residues: 54
  loop : -2.53 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 798 
 TYR   0.013   0.002   TYR G 142 
 PHE   0.022   0.001   PHE G 431 
 TRP   0.014   0.001   TRP G 288 
 HIS   0.003   0.001   HIS G  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7883)
  covalent geometry    : angle       0.53162 (10933)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       1.00050 (    2)
  hydrogen bonds       : bond        0.04153 (  693)
  hydrogen bonds       : angle       3.92928 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.219 
Fit side-chains
REVERT: G  394 LYS cc_start: 0.9780 (tptm) cc_final: 0.9177 (tppp)
REVERT: G  485 GLN cc_start: 0.9296 (tm-30) cc_final: 0.9050 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0448
  time to fit residues: 4.4460
Evaluate side-chains
  53 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 50 optimal weight:   30.0000
   chunk 87 optimal weight:   30.0000
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 70 optimal weight:   50.0000
   chunk 20 optimal weight:    1.9990
   chunk 117 optimal weight:   40.0000
   chunk 94 optimal weight:   20.0000
   overall best weight:    5.9992

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.070915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058670 restraints weight = 56946.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.059589 restraints weight = 41409.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.060234 restraints weight = 31911.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.060733 restraints weight = 26114.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061050 restraints weight = 22202.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7884  Z= 0.167
  Angle     :  0.546   6.987  10935  Z= 0.307
  Chirality :  0.041   0.139   1351
  Planarity :  0.004   0.046   1508
  Dihedral  :  4.229  32.644   1381
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  0.83 (0.24), residues: 1333
  helix:  1.98 (0.17), residues: 899
  sheet: -3.71 (0.56), residues: 53
  loop : -2.44 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.022   0.002   TYR G1219 
 PHE   0.022   0.002   PHE G1204 
 TRP   0.014   0.002   TRP G1297 
 HIS   0.006   0.001   HIS G  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7883)
  covalent geometry    : angle       0.54626 (10933)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.99821 (    2)
  hydrogen bonds       : bond        0.04284 (  693)
  hydrogen bonds       : angle       4.01067 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.301 
Fit side-chains
REVERT: G  485 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8981 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0465
  time to fit residues: 4.6353
Evaluate side-chains
  50 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0070
   chunk 96 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 107 optimal weight:   20.0000
   chunk 78 optimal weight:   40.0000
   chunk 82 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 132 optimal weight:   50.0000
   overall best weight:    4.0004

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.071330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.059106 restraints weight = 56502.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.060004 restraints weight = 41375.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.060666 restraints weight = 32143.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.061099 restraints weight = 26342.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.061472 restraints weight = 22658.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7884  Z= 0.128
  Angle     :  0.507   7.070  10935  Z= 0.278
  Chirality :  0.041   0.129   1351
  Planarity :  0.004   0.044   1508
  Dihedral  :  4.032  32.549   1381
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  1.21 (0.24), residues: 1333
  helix:  2.29 (0.17), residues: 912
  sheet: -3.82 (0.53), residues: 59
  loop : -2.44 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.022   0.002   TYR G 142 
 PHE   0.015   0.001   PHE G 221 
 TRP   0.013   0.001   TRP G 288 
 HIS   0.003   0.001   HIS G 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7883)
  covalent geometry    : angle       0.50650 (10933)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.76109 (    2)
  hydrogen bonds       : bond        0.03977 (  693)
  hydrogen bonds       : angle       3.70123 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.265 
Fit side-chains
REVERT: G  112 MET cc_start: 0.6271 (mtm) cc_final: 0.5946 (ttm)
REVERT: G  485 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8908 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0411
  time to fit residues: 4.0901
Evaluate side-chains
  49 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 113 optimal weight:   40.0000
   chunk 47 optimal weight:   50.0000
   chunk 112 optimal weight:    0.0870
   chunk 71 optimal weight:   50.0000
   chunk 125 optimal weight:   50.0000
   chunk 26 optimal weight:   30.0000
   chunk 24 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 51 optimal weight:   30.0000
   overall best weight:    7.4166

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.069548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.057309 restraints weight = 57078.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.058173 restraints weight = 41655.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058835 restraints weight = 32723.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059313 restraints weight = 26839.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.059627 restraints weight = 22978.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7884  Z= 0.195
  Angle     :  0.572   7.035  10935  Z= 0.324
  Chirality :  0.042   0.145   1351
  Planarity :  0.004   0.048   1508
  Dihedral  :  4.333  32.080   1381
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  0.87 (0.24), residues: 1333
  helix:  2.03 (0.17), residues: 903
  sheet: -3.98 (0.47), residues: 69
  loop : -2.37 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.023   0.002   TYR G 124 
 PHE   0.028   0.002   PHE G 433 
 TRP   0.018   0.002   TRP G1297 
 HIS   0.005   0.001   HIS G 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7883)
  covalent geometry    : angle       0.57144 (10933)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       0.92063 (    2)
  hydrogen bonds       : bond        0.04523 (  693)
  hydrogen bonds       : angle       4.12572 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: G  112 MET cc_start: 0.6597 (mtm) cc_final: 0.6031 (ttm)
REVERT: G  433 PHE cc_start: 0.8767 (m-80) cc_final: 0.8402 (m-80)
REVERT: G  485 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8992 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0421
  time to fit residues: 4.0721
Evaluate side-chains
  47 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 130 optimal weight:   50.0000
   chunk 112 optimal weight:    9.9990
   chunk 125 optimal weight:   50.0000
   chunk 48 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   overall best weight:    6.1788

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.070176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.057989 restraints weight = 57346.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058892 restraints weight = 41654.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.059521 restraints weight = 32368.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.059962 restraints weight = 26677.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.060333 restraints weight = 22982.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7884  Z= 0.163
  Angle     :  0.538   7.119  10935  Z= 0.300
  Chirality :  0.042   0.142   1351
  Planarity :  0.004   0.046   1508
  Dihedral  :  4.185  32.393   1381
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  1.04 (0.24), residues: 1333
  helix:  2.15 (0.17), residues: 913
  sheet: -4.07 (0.49), residues: 59
  loop : -2.45 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.018   0.002   TYR G 142 
 PHE   0.025   0.002   PHE G1182 
 TRP   0.014   0.002   TRP G 288 
 HIS   0.004   0.001   HIS G 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7883)
  covalent geometry    : angle       0.53761 (10933)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.92440 (    2)
  hydrogen bonds       : bond        0.04275 (  693)
  hydrogen bonds       : angle       3.88494 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: G  112 MET cc_start: 0.6533 (mtm) cc_final: 0.5934 (ttm)
REVERT: G  433 PHE cc_start: 0.8827 (m-80) cc_final: 0.8539 (m-80)
REVERT: G  485 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9050 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0557
  time to fit residues: 4.8119
Evaluate side-chains
  49 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 107 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 127 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.070604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.058395 restraints weight = 56283.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.059258 restraints weight = 41231.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.059924 restraints weight = 32271.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.060365 restraints weight = 26539.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.060740 restraints weight = 22945.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7884  Z= 0.141
  Angle     :  0.520   7.005  10935  Z= 0.288
  Chirality :  0.041   0.127   1351
  Planarity :  0.004   0.046   1508
  Dihedral  :  4.057  31.040   1381
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  1.32 (0.24), residues: 1333
  helix:  2.38 (0.17), residues: 907
  sheet: -4.04 (0.49), residues: 59
  loop : -2.30 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.032   0.002   TYR G 142 
 PHE   0.026   0.001   PHE G1182 
 TRP   0.041   0.002   TRP G  75 
 HIS   0.003   0.001   HIS G 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7883)
  covalent geometry    : angle       0.51957 (10933)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.81684 (    2)
  hydrogen bonds       : bond        0.04162 (  693)
  hydrogen bonds       : angle       3.76798 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: G  112 MET cc_start: 0.6508 (mtm) cc_final: 0.5812 (ttm)
REVERT: G  433 PHE cc_start: 0.8758 (m-80) cc_final: 0.8495 (m-80)
REVERT: G  485 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9044 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0449
  time to fit residues: 4.4920
Evaluate side-chains
  49 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 76 optimal weight:   30.0000
   chunk 116 optimal weight:    9.9990
   chunk 127 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 133 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.069987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.057768 restraints weight = 56897.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.058629 restraints weight = 41966.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.059169 restraints weight = 33078.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.059694 restraints weight = 27692.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060004 restraints weight = 23822.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7884  Z= 0.163
  Angle     :  0.537   7.082  10935  Z= 0.300
  Chirality :  0.041   0.136   1351
  Planarity :  0.004   0.046   1508
  Dihedral  :  4.136  31.151   1381
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  1.17 (0.24), residues: 1333
  helix:  2.23 (0.17), residues: 913
  sheet: -3.83 (0.56), residues: 48
  loop : -2.48 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.031   0.002   TYR G 142 
 PHE   0.026   0.002   PHE G1182 
 TRP   0.020   0.002   TRP G  75 
 HIS   0.006   0.001   HIS G  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7883)
  covalent geometry    : angle       0.53707 (10933)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.93379 (    2)
  hydrogen bonds       : bond        0.04275 (  693)
  hydrogen bonds       : angle       3.88462 ( 2037)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.279 
Fit side-chains
REVERT: G  112 MET cc_start: 0.6494 (mtm) cc_final: 0.5924 (ttm)
REVERT: G  433 PHE cc_start: 0.8821 (m-80) cc_final: 0.8521 (m-80)
REVERT: G  485 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9082 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0428
  time to fit residues: 4.1732
Evaluate side-chains
  48 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 73 optimal weight:   40.0000
   chunk 117 optimal weight:   50.0000
   chunk 119 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 130 optimal weight:   50.0000
   chunk 71 optimal weight:   50.0000
   chunk 109 optimal weight:    5.9990
   overall best weight:    8.5990

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

Flipped N/Q/H residues before XYZ refinement:
G 262 ASN
G 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.068313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.056233 restraints weight = 57833.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.057096 restraints weight = 42606.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057695 restraints weight = 33308.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.058095 restraints weight = 27612.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058342 restraints weight = 23998.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7884  Z= 0.219
  Angle     :  0.594   7.578  10935  Z= 0.341
  Chirality :  0.043   0.153   1351
  Planarity :  0.004   0.048   1508
  Dihedral  :  4.527  31.947   1381
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.44 %
    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:  0.71 (0.24), residues: 1333
  helix:  1.87 (0.17), residues: 905
  sheet: -3.93 (0.57), residues: 48
  loop : -2.50 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 798 
 TYR   0.033   0.003   TYR G 142 
 PHE   0.027   0.002   PHE G1182 
 TRP   0.035   0.002   TRP G  75 
 HIS   0.006   0.001   HIS G 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7883)
  covalent geometry    : angle       0.59397 (10933)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       1.19055 (    2)
  hydrogen bonds       : bond        0.04834 (  693)
  hydrogen bonds       : angle       4.34678 ( 2037)

===============================================================================
Job complete
usr+sys time: 1027.93 seconds
wall clock time: 18 minutes 21.16 seconds (1101.16 seconds total)