Starting phenix.real_space_refine
on Wed Feb  4 15:50:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w9d_65771/02_2026/9w9d_65771.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     148      5.49       5
     S      18      5.16       5
     C    6757      2.51       5
     N    2026      2.21       5
     O    2530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11479
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1014, 8301
          Classifications: {'peptide': 1014}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 987}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 761
          Classifications: {'DNA': 37}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 36}
    Chain: "C"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "D"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 2131
          Classifications: {'RNA': 100}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40}
          Link IDs: {'rna2p': 11, 'rna3p': 88}
  Time building chain proxies: 2.71, per 1000 atoms: 0.24
  Number of scatterers: 11479
  At special positions: 0
  Unit cell: (121.362, 118.14, 111.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P     148     15.00
     O    2530      8.00
     N    2026      7.00
     C    6757      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: 0.95
  Conformation dependent library (CDL) restraints added in 430.6 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1928

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      54.6% alpha, 8.4% beta
      58 base pairs and 88 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.358A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 103
      removed outlier: 4.310A  pdb=" N   HIS A  99 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A 103 " --> pdb=" O   HIS A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 3.544A  pdb=" N   GLU A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.648A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 289 through 306
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.782A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 381
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.958A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 3.937A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.594A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 3.988A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.280A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 669
      removed outlier: 3.640A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 697
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 927 through 940
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.163A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.270A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.572A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
      removed outlier: 3.549A  pdb=" N   LYS A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.854A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
      removed outlier: 3.514A  pdb=" N   ASN A1295 " --> pdb=" O   LEU A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1317
      removed outlier: 4.231A  pdb=" N   THR A1314 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LEU A1315 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   THR A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 956
      removed outlier: 6.385A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 760 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A  19 " --> pdb=" O   GLY A   8 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN A1093 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 9.955A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE A1348 " --> pdb=" O   LEU A1203 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.951A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 5.721A  pdb=" N   LYS A1156 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLU A1150 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326

    384 hydrogen bonds defined for protein.
    1122 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      148 hydrogen bonds
      292 hydrogen bond angles
      0 basepair planarities
      58 basepair parallelities
      88 stacking parallelities
  Total time for adding SS restraints: 2.44

  Time building geometry restraints manager: 1.25 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: 2566
        1.33 -     1.45: 3170
        1.45 -     1.57: 5947
        1.57 -     1.69: 296
        1.69 -     1.81: 34
  Bond restraints: 12013
  Sorted by residual:
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.68e+00
  bond pdb=" C3'  DC B  35 "
       pdb=" O3'  DC B  35 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" C4'  DG B  23 "
       pdb=" C3'  DG B  23 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.019 2.00e-02 2.50e+03 8.71e-01
  bond pdb=" C3'  DG C   3 "
       pdb=" C2'  DG C   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 7.63e-01
  bond pdb=" C3'  DA C  13 "
       pdb=" C2'  DA C  13 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 7.10e-01
  ... (remaining 12008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 16505
        1.49 -     2.98: 349
        2.98 -     4.48: 19
        4.48 -     5.97: 4
        5.97 -     7.46: 2
  Bond angle restraints: 16879
  Sorted by residual:
  angle pdb=" C   ALA A1227 "
        pdb=" N   LEU A1228 "
        pdb=" CA  LEU A1228 "
      ideal   model   delta    sigma   weight residual
     122.36  114.90    7.46 2.42e+00 1.71e-01 9.50e+00
  angle pdb=" N   GLY A1103 "
        pdb=" CA  GLY A1103 "
        pdb=" C   GLY A1103 "
      ideal   model   delta    sigma   weight residual
     111.56  113.88   -2.32 1.01e+00 9.80e-01 5.29e+00
  angle pdb=" N   PHE A 478 "
        pdb=" CA  PHE A 478 "
        pdb=" C   PHE A 478 "
      ideal   model   delta    sigma   weight residual
     110.97  113.45   -2.48 1.09e+00 8.42e-01 5.16e+00
  angle pdb=" CB  LYS A 294 "
        pdb=" CG  LYS A 294 "
        pdb=" CD  LYS A 294 "
      ideal   model   delta    sigma   weight residual
     111.30  116.37   -5.07 2.30e+00 1.89e-01 4.85e+00
  angle pdb=" C3'  DG B   7 "
        pdb=" O3'  DG B   7 "
        pdb=" P    DA B   8 "
      ideal   model   delta    sigma   weight residual
     120.20  123.25   -3.05 1.50e+00 4.44e-01 4.15e+00
  ... (remaining 16874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.00: 6832
       32.00 -    64.00: 384
       64.00 -    96.00: 32
       96.00 -   128.00: 0
      128.00 -   160.00: 1
  Dihedral angle restraints: 7249
    sinusoidal: 4271
      harmonic: 2978
  Sorted by residual:
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   60.00  160.00     1      3.50e+01 8.16e-04 1.52e+01
  dihedral pdb=" CA  ASP A 288 "
           pdb=" CB  ASP A 288 "
           pdb=" CG  ASP A 288 "
           pdb=" OD1 ASP A 288 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.95   56.95     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.45  -44.55     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 7246 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1344
       0.028 -    0.055: 395
       0.055 -    0.083: 143
       0.083 -    0.111: 62
       0.111 -    0.138: 9
  Chirality restraints: 1953
  Sorted by residual:
  chirality pdb=" P    DA B   8 "
            pdb=" OP1  DA B   8 "
            pdb=" OP2  DA B   8 "
            pdb=" O5'  DA B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  VAL A 583 "
            pdb=" N   VAL A 583 "
            pdb=" C   VAL A 583 "
            pdb=" CB  VAL A 583 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 1950 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  99 "   -0.030 2.00e-02 2.50e+03   1.45e-02 4.73e+00
        pdb=" N1    U D  99 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    U D  99 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    U D  99 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U D  99 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U D  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U D  99 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    U D  99 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    U D  99 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  98 "   -0.021 2.00e-02 2.50e+03   1.09e-02 2.66e+00
        pdb=" N1    C D  98 "    0.023 2.00e-02 2.50e+03
        pdb=" C2    C D  98 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C D  98 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    C D  98 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C D  98 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4    C D  98 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C D  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  98 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A1229 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 5
        2.02 -     2.74: 988
        2.74 -     3.46: 16308
        3.46 -     4.18: 29983
        4.18 -     4.90: 46910
  Nonbonded interactions: 94194
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 742 "
            pdb=" OP1   C D  69 "
     model   vdw
     1.296 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" N4    C D  20 "
     model   vdw
     1.352 3.200
  nonbonded pdb=" O   GLY A 582 "
            pdb=" C4'  DT B  33 "
     model   vdw
     1.378 3.470
  nonbonded pdb=" CG  GLN A 695 "
            pdb=" O3'  DC B  35 "
     model   vdw
     1.380 3.440
  nonbonded pdb=" O   GLY A 582 "
            pdb=" C5'  DT B  33 "
     model   vdw
     1.841 3.440
  ... (remaining 94189 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.510
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12013  Z= 0.145
  Angle     :  0.517   7.461  16879  Z= 0.306
  Chirality :  0.034   0.138   1953
  Planarity :  0.003   0.040   1596
  Dihedral  : 16.944 159.996   5321
  Min Nonbonded Distance : 1.296

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole:  1.81 (0.27), residues: 1006
  helix:  2.10 (0.23), residues: 501
  sheet:  1.03 (0.61), residues: 69
  loop :  0.23 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.011   0.001   TYR A1242 
 PHE   0.013   0.001   PHE A 970 
 TRP   0.011   0.002   TRP A 464 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (12013)
  covalent geometry    : angle       0.51666 (16879)
  hydrogen bonds       : bond        0.14342 (  532)
  hydrogen bonds       : angle       5.35664 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  515 TYR cc_start: 0.8891 (t80) cc_final: 0.8458 (t80)
REVERT: A  662 LEU cc_start: 0.9049 (mt) cc_final: 0.8799 (mp)
REVERT: A  744 VAL cc_start: 0.9741 (t) cc_final: 0.9473 (t)
REVERT: A  954 LYS cc_start: 0.9421 (mttt) cc_final: 0.9038 (mmtm)
REVERT: A 1317 ASN cc_start: 0.8712 (m-40) cc_final: 0.8407 (m-40)
REVERT: A 1357 GLU cc_start: 0.7878 (pt0) cc_final: 0.7579 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1540
  time to fit residues: 34.9330
Evaluate side-chains
  99 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:   30.0000
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 723 HIS
A 739 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.057456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.048688 restraints weight = 140445.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.049885 restraints weight = 78735.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.050661 restraints weight = 53679.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.051160 restraints weight = 41064.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.051549 restraints weight = 34102.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  12013  Z= 0.168
  Angle     :  0.572   7.743  16879  Z= 0.308
  Chirality :  0.037   0.177   1953
  Planarity :  0.004   0.055   1596
  Dihedral  : 19.363 156.923   3169
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  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 are not related in a simple way.
  whole:  1.36 (0.26), residues: 1006
  helix:  1.68 (0.23), residues: 518
  sheet:  1.75 (0.68), residues: 57
  loop : -0.13 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 661 
 TYR   0.012   0.002   TYR A  72 
 PHE   0.018   0.002   PHE A  32 
 TRP   0.012   0.002   TRP A 659 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12013)
  covalent geometry    : angle       0.57218 (16879)
  hydrogen bonds       : bond        0.04753 (  532)
  hydrogen bonds       : angle       4.47826 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.8616 (m-10) cc_final: 0.8318 (m-10)
REVERT: A   82 LEU cc_start: 0.9857 (tt) cc_final: 0.9392 (tp)
REVERT: A   86 PHE cc_start: 0.9738 (m-80) cc_final: 0.9494 (m-10)
REVERT: A   90 MET cc_start: 0.9052 (ppp) cc_final: 0.8752 (ttp)
REVERT: A  161 MET cc_start: 0.9844 (ttt) cc_final: 0.9377 (tpp)
REVERT: A  163 LYS cc_start: 0.8980 (pttm) cc_final: 0.8776 (pttp)
REVERT: A  450 TYR cc_start: 0.9125 (p90) cc_final: 0.8634 (p90)
REVERT: A  587 PHE cc_start: 0.9421 (m-10) cc_final: 0.9139 (m-80)
REVERT: A  694 MET cc_start: 0.9349 (tpt) cc_final: 0.8897 (tpp)
REVERT: A 1089 MET cc_start: 0.7440 (tpp) cc_final: 0.7141 (tpp)
REVERT: A 1099 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9257 (mp0)
REVERT: A 1134 PHE cc_start: 0.9710 (m-80) cc_final: 0.9487 (m-80)
REVERT: A 1204 PHE cc_start: 0.9815 (m-80) cc_final: 0.9481 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1287
  time to fit residues: 17.9926
Evaluate side-chains
  73 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 99 optimal weight:   30.0000
   chunk 19 optimal weight:    0.0010
   chunk 18 optimal weight:   30.0000
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    4.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.053881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.045264 restraints weight = 145920.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.046428 restraints weight = 82440.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.047197 restraints weight = 56232.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.047698 restraints weight = 43047.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.048064 restraints weight = 35748.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12013  Z= 0.159
  Angle     :  0.538   6.971  16879  Z= 0.292
  Chirality :  0.036   0.166   1953
  Planarity :  0.004   0.048   1596
  Dihedral  : 19.501 154.976   3169
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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 are not related in a simple way.
  whole:  1.08 (0.26), residues: 1006
  helix:  1.33 (0.22), residues: 526
  sheet:  1.39 (0.59), residues: 69
  loop : -0.11 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  71 
 TYR   0.013   0.001   TYR A1201 
 PHE   0.014   0.002   PHE A 970 
 TRP   0.008   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12013)
  covalent geometry    : angle       0.53815 (16879)
  hydrogen bonds       : bond        0.04210 (  532)
  hydrogen bonds       : angle       4.34659 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.9712 (m-10) cc_final: 0.9148 (t80)
REVERT: A   90 MET cc_start: 0.9022 (ppp) cc_final: 0.7249 (ttt)
REVERT: A  450 TYR cc_start: 0.8985 (p90) cc_final: 0.8615 (p90)
REVERT: A  587 PHE cc_start: 0.9510 (m-10) cc_final: 0.9105 (m-80)
REVERT: A  631 MET cc_start: 0.9525 (tpt) cc_final: 0.9197 (tpp)
REVERT: A  939 MET cc_start: 0.6485 (ptt) cc_final: 0.5970 (ptt)
REVERT: A 1089 MET cc_start: 0.7287 (tpp) cc_final: 0.6928 (tpp)
REVERT: A 1204 PHE cc_start: 0.9816 (m-80) cc_final: 0.9423 (m-80)
REVERT: A 1213 MET cc_start: 0.9684 (tpt) cc_final: 0.9373 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1097
  time to fit residues: 12.7398
Evaluate side-chains
  66 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 94 optimal weight:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 80 optimal weight:   30.0000
   chunk 17 optimal weight:   40.0000
   chunk 22 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    8.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 129 HIS
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.046544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.038281 restraints weight = 159413.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.039321 restraints weight = 91130.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.039990 restraints weight = 63396.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.040452 restraints weight = 49395.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.040740 restraints weight = 41235.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.5708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092  12013  Z= 0.260
  Angle     :  0.695   8.043  16879  Z= 0.379
  Chirality :  0.041   0.258   1953
  Planarity :  0.005   0.064   1596
  Dihedral  : 20.122 148.952   3169
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 22.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.65 %
    Favored  : 98.24 %
  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 are not related in a simple way.
  whole:  0.02 (0.25), residues: 1006
  helix:  0.33 (0.21), residues: 520
  sheet:  0.87 (0.58), residues: 71
  loop : -0.40 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 629 
 TYR   0.022   0.002   TYR A 515 
 PHE   0.022   0.003   PHE A 970 
 TRP   0.014   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (12013)
  covalent geometry    : angle       0.69526 (16879)
  hydrogen bonds       : bond        0.06637 (  532)
  hydrogen bonds       : angle       4.75340 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.9818 (tt) cc_final: 0.9578 (tp)
REVERT: A   86 PHE cc_start: 0.9709 (m-10) cc_final: 0.9457 (m-10)
REVERT: A  161 MET cc_start: 0.9873 (ttt) cc_final: 0.9370 (tpp)
REVERT: A  163 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8707 (pttm)
REVERT: A  164 PHE cc_start: 0.9562 (m-80) cc_final: 0.9151 (m-80)
REVERT: A  587 PHE cc_start: 0.9473 (m-10) cc_final: 0.9198 (m-10)
REVERT: A 1171 ARG cc_start: 0.9621 (ttt180) cc_final: 0.9390 (ttp80)
REVERT: A 1204 PHE cc_start: 0.9811 (m-80) cc_final: 0.9367 (m-80)
REVERT: A 1213 MET cc_start: 0.9723 (tpt) cc_final: 0.9383 (tmm)
REVERT: A 1312 LEU cc_start: 0.9740 (tt) cc_final: 0.9511 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.1146
  time to fit residues: 12.2492
Evaluate side-chains
  55 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:   40.0000
   chunk 3 optimal weight:   20.0000
   chunk 43 optimal weight:   30.0000
   chunk 28 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:   30.0000
   chunk 92 optimal weight:    0.9980
   chunk 46 optimal weight:   40.0000
   chunk 84 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   chunk 71 optimal weight:   40.0000
   overall best weight:    8.9992

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
A 739 GLN
A1101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.044971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.036787 restraints weight = 161310.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.037770 restraints weight = 93165.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.038397 restraints weight = 65408.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.038861 restraints weight = 51470.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.039187 restraints weight = 42977.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.6597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  12013  Z= 0.251
  Angle     :  0.663   6.720  16879  Z= 0.365
  Chirality :  0.040   0.213   1953
  Planarity :  0.004   0.046   1596
  Dihedral  : 20.426 145.681   3169
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 22.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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 are not related in a simple way.
  whole: -0.25 (0.25), residues: 1006
  helix:  0.13 (0.22), residues: 516
  sheet:  0.54 (0.58), residues: 71
  loop : -0.52 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 557 
 TYR   0.026   0.002   TYR A 515 
 PHE   0.019   0.002   PHE A 446 
 TRP   0.009   0.002   TRP A 659 
 HIS   0.008   0.002   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (12013)
  covalent geometry    : angle       0.66296 (16879)
  hydrogen bonds       : bond        0.05858 (  532)
  hydrogen bonds       : angle       4.65699 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.9717 (tt) cc_final: 0.9326 (tt)
REVERT: A   86 PHE cc_start: 0.9284 (m-10) cc_final: 0.8985 (m-10)
REVERT: A  161 MET cc_start: 0.9685 (ttt) cc_final: 0.8959 (tpp)
REVERT: A  163 LYS cc_start: 0.9274 (ptpp) cc_final: 0.8850 (ptpp)
REVERT: A  164 PHE cc_start: 0.9471 (m-80) cc_final: 0.9105 (m-80)
REVERT: A  495 MET cc_start: 0.9309 (mpp) cc_final: 0.9079 (tpp)
REVERT: A  523 GLU cc_start: 0.8806 (tt0) cc_final: 0.8559 (pt0)
REVERT: A  587 PHE cc_start: 0.9331 (m-10) cc_final: 0.8745 (m-10)
REVERT: A  631 MET cc_start: 0.9525 (tpt) cc_final: 0.9324 (tpp)
REVERT: A  694 MET cc_start: 0.9356 (tpt) cc_final: 0.9014 (tpp)
REVERT: A  954 LYS cc_start: 0.9167 (pttp) cc_final: 0.8943 (ptmm)
REVERT: A 1204 PHE cc_start: 0.9724 (m-80) cc_final: 0.9172 (m-80)
REVERT: A 1213 MET cc_start: 0.9544 (tpt) cc_final: 0.9342 (tmm)
REVERT: A 1312 LEU cc_start: 0.9646 (tt) cc_final: 0.9386 (mt)
REVERT: A 1317 ASN cc_start: 0.9126 (m110) cc_final: 0.8883 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1099
  time to fit residues: 10.3507
Evaluate side-chains
  53 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 3 optimal weight:   30.0000
   chunk 7 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 10 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    8.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 489 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.036413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.025484 restraints weight = 156124.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.026420 restraints weight = 98507.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.027066 restraints weight = 73149.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.027518 restraints weight = 59576.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.027817 restraints weight = 51617.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.7333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  12013  Z= 0.246
  Angle     :  0.657   6.750  16879  Z= 0.360
  Chirality :  0.040   0.250   1953
  Planarity :  0.004   0.046   1596
  Dihedral  : 20.475 142.688   3169
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 23.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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 are not related in a simple way.
  whole: -0.46 (0.25), residues: 1006
  helix: -0.03 (0.22), residues: 514
  sheet: -0.26 (0.60), residues: 66
  loop : -0.48 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 557 
 TYR   0.023   0.002   TYR A 515 
 PHE   0.025   0.002   PHE A  97 
 TRP   0.015   0.003   TRP A1126 
 HIS   0.011   0.002   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (12013)
  covalent geometry    : angle       0.65705 (16879)
  hydrogen bonds       : bond        0.06093 (  532)
  hydrogen bonds       : angle       4.68195 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.9739 (m-10) cc_final: 0.9425 (m-80)
REVERT: A  161 MET cc_start: 0.9834 (ttt) cc_final: 0.9402 (tpp)
REVERT: A  163 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8748 (ptpp)
REVERT: A  164 PHE cc_start: 0.9479 (m-80) cc_final: 0.9197 (m-80)
REVERT: A  587 PHE cc_start: 0.8875 (m-10) cc_final: 0.8617 (m-10)
REVERT: A 1204 PHE cc_start: 0.9624 (m-80) cc_final: 0.9340 (m-80)
REVERT: A 1213 MET cc_start: 0.9745 (tpt) cc_final: 0.9478 (tmm)
REVERT: A 1312 LEU cc_start: 0.9603 (tt) cc_final: 0.9396 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0942
  time to fit residues: 7.8054
Evaluate side-chains
  49 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:    0.0370
   chunk 45 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 91 optimal weight:   30.0000
   chunk 77 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 110 optimal weight:   20.0000
   chunk 114 optimal weight:   20.0000
   overall best weight:    7.8070

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.038471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.027342 restraints weight = 146619.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.028249 restraints weight = 95333.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.028882 restraints weight = 72034.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.029333 restraints weight = 59338.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.029626 restraints weight = 51596.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.7863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  12013  Z= 0.222
  Angle     :  0.617   6.478  16879  Z= 0.340
  Chirality :  0.039   0.203   1953
  Planarity :  0.004   0.044   1596
  Dihedral  : 20.540 141.861   3169
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 21.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  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 are not related in a simple way.
  whole: -0.36 (0.26), residues: 1006
  helix:  0.08 (0.22), residues: 505
  sheet: -0.37 (0.60), residues: 64
  loop : -0.43 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 557 
 TYR   0.021   0.002   TYR A 515 
 PHE   0.017   0.002   PHE A  98 
 TRP   0.011   0.002   TRP A 659 
 HIS   0.007   0.002   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (12013)
  covalent geometry    : angle       0.61722 (16879)
  hydrogen bonds       : bond        0.05400 (  532)
  hydrogen bonds       : angle       4.66427 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.9766 (m-10) cc_final: 0.9467 (m-80)
REVERT: A  138 LEU cc_start: 0.9854 (tp) cc_final: 0.9643 (pp)
REVERT: A  161 MET cc_start: 0.9865 (ttt) cc_final: 0.9384 (tpp)
REVERT: A  163 LYS cc_start: 0.9188 (ptpp) cc_final: 0.8760 (ptpp)
REVERT: A  164 PHE cc_start: 0.9523 (m-80) cc_final: 0.9215 (m-80)
REVERT: A  587 PHE cc_start: 0.8877 (m-10) cc_final: 0.8650 (m-10)
REVERT: A 1204 PHE cc_start: 0.9683 (m-80) cc_final: 0.9378 (m-80)
REVERT: A 1213 MET cc_start: 0.9770 (tpt) cc_final: 0.9504 (tmm)
REVERT: A 1312 LEU cc_start: 0.9604 (tt) cc_final: 0.9373 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1079
  time to fit residues: 8.9922
Evaluate side-chains
  46 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 42 optimal weight:   40.0000
   chunk 72 optimal weight:   30.0000
   chunk 9 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 110 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 723 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 = 0.2994 r_free = 0.2994 target = 0.036328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.025927 restraints weight = 152570.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.026879 restraints weight = 94887.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.027541 restraints weight = 69438.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.027985 restraints weight = 55927.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.028325 restraints weight = 48131.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.8217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  12013  Z= 0.211
  Angle     :  0.612   9.782  16879  Z= 0.335
  Chirality :  0.038   0.173   1953
  Planarity :  0.004   0.041   1596
  Dihedral  : 20.517 141.224   3169
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 21.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  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 are not related in a simple way.
  whole: -0.36 (0.26), residues: 1006
  helix:  0.14 (0.22), residues: 505
  sheet: -0.58 (0.60), residues: 66
  loop : -0.49 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 557 
 TYR   0.020   0.002   TYR A 515 
 PHE   0.018   0.002   PHE A  97 
 TRP   0.012   0.002   TRP A 659 
 HIS   0.007   0.002   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (12013)
  covalent geometry    : angle       0.61162 (16879)
  hydrogen bonds       : bond        0.05351 (  532)
  hydrogen bonds       : angle       4.63317 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.9732 (m-10) cc_final: 0.9496 (m-80)
REVERT: A  138 LEU cc_start: 0.9820 (tp) cc_final: 0.9609 (pp)
REVERT: A  161 MET cc_start: 0.9853 (ttt) cc_final: 0.9437 (tpp)
REVERT: A  163 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8680 (ptpp)
REVERT: A  164 PHE cc_start: 0.9492 (m-80) cc_final: 0.9191 (m-80)
REVERT: A  587 PHE cc_start: 0.8513 (m-10) cc_final: 0.8302 (m-10)
REVERT: A 1204 PHE cc_start: 0.9635 (m-80) cc_final: 0.9387 (m-80)
REVERT: A 1312 LEU cc_start: 0.9564 (tt) cc_final: 0.9337 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0923
  time to fit residues: 7.9013
Evaluate side-chains
  49 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   chunk 58 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 79 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 110 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   overall best weight:    6.2992

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 723 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 = 0.2975 r_free = 0.2975 target = 0.034283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.024372 restraints weight = 151993.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.025352 restraints weight = 92969.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.026042 restraints weight = 66816.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.026538 restraints weight = 52978.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.026885 restraints weight = 44707.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.8516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12013  Z= 0.186
  Angle     :  0.575   7.763  16879  Z= 0.315
  Chirality :  0.037   0.182   1953
  Planarity :  0.003   0.040   1596
  Dihedral  : 20.489 144.026   3169
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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 are not related in a simple way.
  whole: -0.16 (0.26), residues: 1006
  helix:  0.37 (0.22), residues: 504
  sheet: -0.30 (0.61), residues: 65
  loop : -0.51 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 557 
 TYR   0.018   0.002   TYR A 515 
 PHE   0.013   0.002   PHE A  97 
 TRP   0.015   0.002   TRP A 659 
 HIS   0.006   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12013)
  covalent geometry    : angle       0.57452 (16879)
  hydrogen bonds       : bond        0.04785 (  532)
  hydrogen bonds       : angle       4.50914 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.9803 (tp) cc_final: 0.9596 (pp)
REVERT: A  161 MET cc_start: 0.9843 (ttt) cc_final: 0.9424 (tpp)
REVERT: A  163 LYS cc_start: 0.9092 (ptpp) cc_final: 0.8671 (ptpp)
REVERT: A  164 PHE cc_start: 0.9469 (m-80) cc_final: 0.9181 (m-80)
REVERT: A 1204 PHE cc_start: 0.9601 (m-80) cc_final: 0.9324 (m-80)
REVERT: A 1312 LEU cc_start: 0.9493 (tt) cc_final: 0.9246 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0903
  time to fit residues: 8.1378
Evaluate side-chains
  46 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 4 optimal weight:   30.0000
   chunk 0 optimal weight:   40.0000
   chunk 26 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.036776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.026142 restraints weight = 151686.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.027114 restraints weight = 94297.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.027766 restraints weight = 69256.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.028211 restraints weight = 56127.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.028531 restraints weight = 48518.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.8815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  12013  Z= 0.212
  Angle     :  0.608  10.160  16879  Z= 0.333
  Chirality :  0.038   0.269   1953
  Planarity :  0.004   0.039   1596
  Dihedral  : 20.586 146.328   3169
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 21.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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 are not related in a simple way.
  whole: -0.33 (0.26), residues: 1006
  helix:  0.22 (0.22), residues: 507
  sheet: -0.67 (0.62), residues: 68
  loop : -0.52 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 557 
 TYR   0.019   0.002   TYR A 515 
 PHE   0.013   0.002   PHE A 643 
 TRP   0.014   0.002   TRP A 659 
 HIS   0.007   0.002   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (12013)
  covalent geometry    : angle       0.60830 (16879)
  hydrogen bonds       : bond        0.05336 (  532)
  hydrogen bonds       : angle       4.59774 ( 1414)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8812 (tpp) cc_final: 0.8571 (tpp)
REVERT: A  138 LEU cc_start: 0.9804 (tp) cc_final: 0.9588 (pp)
REVERT: A  161 MET cc_start: 0.9834 (ttt) cc_final: 0.9398 (tpp)
REVERT: A  163 LYS cc_start: 0.9087 (ptpp) cc_final: 0.8662 (ptpp)
REVERT: A  164 PHE cc_start: 0.9464 (m-80) cc_final: 0.9160 (m-80)
REVERT: A 1204 PHE cc_start: 0.9510 (m-80) cc_final: 0.9293 (m-80)
REVERT: A 1312 LEU cc_start: 0.9498 (tt) cc_final: 0.9254 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0789
  time to fit residues: 6.7428
Evaluate side-chains
  44 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 71 optimal weight:   40.0000
   chunk 39 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.036497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.025692 restraints weight = 148489.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.026680 restraints weight = 92301.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.027371 restraints weight = 67517.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.027857 restraints weight = 54312.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.028200 restraints weight = 46561.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.8812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12013  Z= 0.140
  Angle     :  0.523   8.657  16879  Z= 0.286
  Chirality :  0.036   0.235   1953
  Planarity :  0.003   0.037   1596
  Dihedral  : 20.294 151.862   3169
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole:  0.11 (0.26), residues: 1006
  helix:  0.72 (0.23), residues: 504
  sheet: -0.49 (0.63), residues: 66
  loop : -0.49 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 661 
 TYR   0.013   0.001   TYR A 515 
 PHE   0.009   0.001   PHE A 539 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.007   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12013)
  covalent geometry    : angle       0.52298 (16879)
  hydrogen bonds       : bond        0.03962 (  532)
  hydrogen bonds       : angle       4.27045 ( 1414)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1689.61 seconds
wall clock time: 30 minutes 12.30 seconds (1812.30 seconds total)