Starting phenix.real_space_refine
on Fri Dec  8 04:36:48 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxa_10337/12_2023/6sxa_10337.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4499      2.51       5
     N    1219      2.21       5
     O    1271      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "F TYR   46": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  118": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  134": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  153": "NH1" <-> "NH2"
    Residue "F GLU  179": "OE1" <-> "OE2"
    Residue "F ARG  195": "NH1" <-> "NH2"
    Residue "F GLU  239": "OE1" <-> "OE2"
    Residue "F TYR  297": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  301": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  314": "NH1" <-> "NH2"
    Residue "F ARG  415": "NH1" <-> "NH2"
    Residue "F TYR  564": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  581": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  606": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  799": "NH1" <-> "NH2"
    Residue "F PHE  851": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7014
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 5620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 5620
          Classifications: {'peptide': 747}
          Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 104}
          Link IDs: {'PTRANS': 34, 'TRANS': 712}
          Chain breaks: 3
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 389
          Unresolved non-hydrogen angles: 468
          Unresolved non-hydrogen dihedrals: 321
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 225
    Chain: "G"
      Number of atoms: 1394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1394
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 98
  Time building chain proxies: 4.36, per 1000 atoms: 0.62
  Number of scatterers: 7014
  At special positions: 0
  Unit cell: (84.18, 111.78, 128.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1271      8.00
     N    1219      7.00
     C    4499      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      52.6% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'F' and resid 16 through 29
      removed outlier: 4.034A  pdb=" N   LEU F  22 " --> pdb=" O   TYR F  18 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU F  24 " --> pdb=" O   ARG F  20 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASP F  28 " --> pdb=" O   LEU F  24 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   THR F  29 " --> pdb=" O   GLU F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 53
      removed outlier: 3.544A  pdb=" N   LEU F  44 " --> pdb=" O   GLY F  40 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU F  45 " --> pdb=" O   ALA F  41 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR F  46 " --> pdb=" O   ASP F  42 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS F  47 " --> pdb=" O   ARG F  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 65 through 80
      removed outlier: 3.875A  pdb=" N   GLU F  69 " --> pdb=" O   GLN F  65 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU F  70 " --> pdb=" O   PRO F  66 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR F  71 " --> pdb=" O   ALA F  67 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU F  79 " --> pdb=" O   GLN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 98
      removed outlier: 4.214A  pdb=" N   ARG F  97 " --> pdb=" O   THR F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 104
    Processing helix  chain 'F' and resid 110 through 121
      removed outlier: 3.797A  pdb=" N   LEU F 114 " --> pdb=" O   THR F 110 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL F 115 " --> pdb=" O   SER F 111 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL F 116 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP F 117 " --> pdb=" O   ILE F 113 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 135 through 141
      removed outlier: 3.544A  pdb=" N   GLU F 141 " --> pdb=" O   ARG F 138 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 153
      removed outlier: 4.022A  pdb=" N   PHE F 147 " --> pdb=" O   CYS F 143 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 185
    Processing helix  chain 'F' and resid 197 through 202
      removed outlier: 4.015A  pdb=" N   SER F 202 " --> pdb=" O   VAL F 198 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 207
      removed outlier: 4.057A  pdb=" N   GLN F 206 " --> pdb=" O   SER F 202 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   HIS F 207 " --> pdb=" O   PHE F 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 202 through 207'
    Processing helix  chain 'F' and resid 222 through 243
      removed outlier: 4.281A  pdb=" N   ALA F 228 " --> pdb=" O   ALA F 224 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP F 231 " --> pdb=" O   THR F 227 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS F 238 " --> pdb=" O   ASN F 234 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLU F 239 " --> pdb=" O   ALA F 235 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   HIS F 243 " --> pdb=" O   GLU F 239 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 254 through 259
      removed outlier: 3.701A  pdb=" N   ILE F 258 " --> pdb=" O   LEU F 254 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   GLY F 259 " --> pdb=" O   GLU F 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 254 through 259'
    Processing helix  chain 'F' and resid 262 through 270
      removed outlier: 3.563A  pdb=" N   ILE F 266 " --> pdb=" O   PHE F 262 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 280 through 301
      removed outlier: 4.270A  pdb=" N   GLN F 286 " --> pdb=" O   LYS F 282 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU F 295 " --> pdb=" O   LEU F 291 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLN F 296 " --> pdb=" O   ARG F 292 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   SER F 299 " --> pdb=" O   LEU F 295 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN F 300 " --> pdb=" O   GLN F 296 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 313
    Processing helix  chain 'F' and resid 333 through 344
      removed outlier: 3.890A  pdb=" N   ARG F 342 " --> pdb=" O   ASN F 338 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL F 343 " --> pdb=" O   ALA F 339 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 379 through 397
      removed outlier: 3.911A  pdb=" N   THR F 385 " --> pdb=" O   TRP F 381 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU F 386 " --> pdb=" O   GLU F 382 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL F 387 " --> pdb=" O   ALA F 383 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS F 389 " --> pdb=" O   THR F 385 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU F 392 " --> pdb=" O   LEU F 388 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA F 393 " --> pdb=" O   LYS F 389 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 398 through 403
      removed outlier: 4.033A  pdb=" N   GLY F 403 " --> pdb=" O   GLU F 399 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 413 through 426
    Processing helix  chain 'F' and resid 427 through 440
      removed outlier: 3.809A  pdb=" N   PHE F 431 " --> pdb=" O   GLY F 427 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU F 432 " --> pdb=" O   ALA F 428 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 565 through 573
    Processing helix  chain 'F' and resid 584 through 595
      removed outlier: 3.940A  pdb=" N   VAL F 588 " --> pdb=" O   GLU F 584 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN F 590 " --> pdb=" O   THR F 586 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU F 592 " --> pdb=" O   VAL F 588 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 613 through 638
      removed outlier: 3.786A  pdb=" N   ALA F 622 " --> pdb=" O   ARG F 618 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU F 631 " --> pdb=" O   LYS F 627 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU F 633 " --> pdb=" O   ALA F 629 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE F 634 " --> pdb=" O   PHE F 630 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG F 635 " --> pdb=" O   GLU F 631 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 689 through 692
      removed outlier: 4.015A  pdb=" N   ARG F 692 " --> pdb=" O   ARG F 689 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 689 through 692'
    Processing helix  chain 'F' and resid 694 through 700
    Processing helix  chain 'F' and resid 729 through 738
      removed outlier: 3.688A  pdb=" N   ILE F 733 " --> pdb=" O   ILE F 729 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN F 737 " --> pdb=" O   ILE F 733 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 741 through 752
      removed outlier: 3.731A  pdb=" N   ILE F 746 " --> pdb=" O   TYR F 742 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   SER F 747 " --> pdb=" O   SER F 743 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG F 750 " --> pdb=" O   ILE F 746 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 771 through 778
    Processing helix  chain 'F' and resid 783 through 795
      removed outlier: 3.850A  pdb=" N   HIS F 794 " --> pdb=" O   LEU F 790 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE F 795 " --> pdb=" O   LEU F 791 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 805 through 817
      removed outlier: 4.326A  pdb=" N   ALA F 810 " --> pdb=" O   PRO F 806 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU F 811 " --> pdb=" O   HIS F 807 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU F 814 " --> pdb=" O   ALA F 810 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 827 through 832
      removed outlier: 4.449A  pdb=" N   THR F 832 " --> pdb=" O   ALA F 828 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 847 through 855
      removed outlier: 3.958A  pdb=" N   PHE F 851 " --> pdb=" O   GLY F 847 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LYS F 854 " --> pdb=" O   ASP F 850 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET F 855 " --> pdb=" O   PHE F 851 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 859 through 868
    Processing helix  chain 'F' and resid 880 through 889
    Processing helix  chain 'F' and resid 891 through 902
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.700A  pdb=" N   VAL G 116 " --> pdb=" O   LEU G 113 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 143 through 149
    Processing helix  chain 'G' and resid 152 through 161
      removed outlier: 4.143A  pdb=" N   GLN G 158 " --> pdb=" O   HIS G 154 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER G 159 " --> pdb=" O   GLY G 155 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU G 160 " --> pdb=" O   ARG G 156 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLY G 161 " --> pdb=" O   LEU G 157 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 180 through 191
      removed outlier: 3.944A  pdb=" N   LYS G 187 " --> pdb=" O   LYS G 183 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU G 191 " --> pdb=" O   LYS G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 203 through 214
      removed outlier: 3.905A  pdb=" N   ARG G 207 " --> pdb=" O   GLU G 203 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LYS G 213 " --> pdb=" O   LEU G 209 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 230 through 239
    Processing helix  chain 'G' and resid 240 through 242
      No H-bonds generated for 'chain 'G' and resid 240 through 242'
    Processing helix  chain 'G' and resid 246 through 255
      removed outlier: 3.585A  pdb=" N   SER G 250 " --> pdb=" O   ASN G 246 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 259 through 264
    Processing helix  chain 'G' and resid 269 through 273
      removed outlier: 3.883A  pdb=" N   LEU G 273 " --> pdb=" O   ASP G 270 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 278 through 289
    Processing sheet with id=AA1, first strand: chain 'F' and resid 86 through 87
      removed outlier: 7.163A  pdb=" N   ARG F  86 " --> pdb=" O   PHE F 108 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL F  59 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LEU F  58 " --> pdb=" O   GLY F 130 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   LEU F 132 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU F  60 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   PHE F 164 " --> pdb=" O   VAL F 133 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   VAL F  33 " --> pdb=" O   THR F 165 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU F  32 " --> pdb=" O   TYR F 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 214 through 216
    Processing sheet with id=AA3, first strand: chain 'F' and resid 410 through 411
      removed outlier: 3.770A  pdb=" N   ALA F 411 " --> pdb=" O   HIS F 555 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 705 through 709
      removed outlier: 3.865A  pdb=" N   GLU F 707 " --> pdb=" O   ILE F 684 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   VAL F 685 " --> pdb=" O   ILE F 717 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE F 717 " --> pdb=" O   VAL F 685 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 723 through 728
      removed outlier: 4.001A  pdb=" N   GLU F 725 " --> pdb=" O   VAL F 756 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU F 758 " --> pdb=" O   GLU F 725 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU F 760 " --> pdb=" O   LYS F 727 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   LEU F 801 " --> pdb=" O   PRO F 755 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU F 757 " --> pdb=" O   LEU F 801 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   CYS F 803 " --> pdb=" O   LEU F 757 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ILE F 759 " --> pdb=" O   CYS F 803 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 121 through 123
      removed outlier: 3.770A  pdb=" N   TYR G 130 " --> pdb=" O   ALA G 138 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR G 136 " --> pdb=" O   LEU G 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 140 through 142
      removed outlier: 6.705A  pdb=" N   LEU G 141 " --> pdb=" O   GLN G 172 " (cutoff:3.500A)

    253 hydrogen bonds defined for protein.
    744 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.86

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1238
        1.32 -     1.44: 1766
        1.44 -     1.57: 4121
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 7157
  Sorted by residual:
  bond pdb=" C   SER G 104 "
       pdb=" N   PRO G 105 "
    ideal  model  delta    sigma   weight residual
    1.337  1.378 -0.041 9.80e-03 1.04e+04 1.76e+01
  bond pdb=" C   LEU F  84 "
       pdb=" N   PRO F  85 "
    ideal  model  delta    sigma   weight residual
    1.331  1.379 -0.048 1.20e-02 6.94e+03 1.61e+01
  bond pdb=" C   ASP F 271 "
       pdb=" N   PRO F 272 "
    ideal  model  delta    sigma   weight residual
    1.333  1.372 -0.039 1.01e-02 9.80e+03 1.46e+01
  bond pdb=" N   GLN F  65 "
       pdb=" CA  GLN F  65 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 9.20e-03 1.18e+04 1.37e+01
  bond pdb=" N   VAL F 709 "
       pdb=" CA  VAL F 709 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.07e-02 8.73e+03 1.21e+01
  ... (remaining 7152 not shown)

  Histogram of bond angle deviations from ideal:
       98.37 -   105.50: 170
      105.50 -   112.63: 3805
      112.63 -   119.76: 2674
      119.76 -   126.89: 3053
      126.89 -   134.01: 70
  Bond angle restraints: 9772
  Sorted by residual:
  angle pdb=" N   GLU F  68 "
        pdb=" CA  GLU F  68 "
        pdb=" C   GLU F  68 "
      ideal   model   delta    sigma   weight residual
     111.28  103.47    7.81 1.09e+00 8.42e-01 5.14e+01
  angle pdb=" N   PRO F  14 "
        pdb=" CA  PRO F  14 "
        pdb=" CB  PRO F  14 "
      ideal   model   delta    sigma   weight residual
     103.36  109.47   -6.11 8.80e-01 1.29e+00 4.82e+01
  angle pdb=" N   GLN F 206 "
        pdb=" CA  GLN F 206 "
        pdb=" C   GLN F 206 "
      ideal   model   delta    sigma   weight residual
     111.28  104.43    6.85 1.09e+00 8.42e-01 3.95e+01
  angle pdb=" C   PRO F  66 "
        pdb=" CA  PRO F  66 "
        pdb=" CB  PRO F  66 "
      ideal   model   delta    sigma   weight residual
     113.06  103.18    9.88 1.59e+00 3.96e-01 3.86e+01
  angle pdb=" N   PRO F 347 "
        pdb=" CA  PRO F 347 "
        pdb=" CB  PRO F 347 "
      ideal   model   delta    sigma   weight residual
     103.38  109.80   -6.42 1.05e+00 9.07e-01 3.74e+01
  ... (remaining 9767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3835
       17.85 -    35.69: 352
       35.69 -    53.54: 88
       53.54 -    71.39: 15
       71.39 -    89.23: 4
  Dihedral angle restraints: 4294
    sinusoidal: 1517
      harmonic: 2777
  Sorted by residual:
  dihedral pdb=" CA  GLU F 394 "
           pdb=" C   GLU F 394 "
           pdb=" N   ASN F 395 "
           pdb=" CA  ASN F 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.17   25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  CYS F 143 "
           pdb=" C   CYS F 143 "
           pdb=" N   GLN F 144 "
           pdb=" CA  GLN F 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.47  -25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  VAL F  61 "
           pdb=" C   VAL F  61 "
           pdb=" N   LEU F  62 "
           pdb=" CA  LEU F  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.11  -24.89     0      5.00e+00 4.00e-02 2.48e+01
  ... (remaining 4291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 792
       0.075 -    0.149: 271
       0.149 -    0.224: 90
       0.224 -    0.299: 17
       0.299 -    0.373: 8
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CA  GLU F 836 "
            pdb=" N   GLU F 836 "
            pdb=" C   GLU F 836 "
            pdb=" CB  GLU F 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CA  GLU F  69 "
            pdb=" N   GLU F  69 "
            pdb=" C   GLU F  69 "
            pdb=" CB  GLU F  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  GLN F 206 "
            pdb=" N   GLN F 206 "
            pdb=" C   GLN F 206 "
            pdb=" CB  GLN F 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1175 not shown)

  Planarity restraints: 1249
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 719 "    0.055 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO F 720 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO F 720 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO F 720 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS F  35 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.47e+00
        pdb=" C   CYS F  35 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   CYS F  35 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA F  36 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F 160 "   -0.012 2.00e-02 2.50e+03   2.37e-02 5.63e+00
        pdb=" C   PHE F 160 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE F 160 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE F 161 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1246 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1479
        2.78 -     3.31: 6795
        3.31 -     3.84: 10235
        3.84 -     4.37: 11496
        4.37 -     4.90: 18828
  Nonbonded interactions: 48833
  Sorted by model distance:
  nonbonded pdb=" O   LEU F 149 "
            pdb=" N   PHE F 152 "
     model   vdw
     2.245 2.520
  nonbonded pdb=" N   ASP F 850 "
            pdb=" OD1 ASP F 850 "
     model   vdw
     2.257 2.520
  nonbonded pdb=" N   GLU F 179 "
            pdb=" OE1 GLU F 179 "
     model   vdw
     2.297 2.520
  nonbonded pdb=" O   ARG G 207 "
            pdb=" OG1 THR G 211 "
     model   vdw
     2.322 2.440
  nonbonded pdb=" O   SER F 332 "
            pdb=" OG  SER F 332 "
     model   vdw
     2.337 2.440
  ... (remaining 48828 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.040
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     22.380
  Find NCS groups from input model:        0.190
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
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      :  0.010   0.061   7157  Z= 0.652
  Angle     :  1.370   9.943   9772  Z= 0.985
  Chirality :  0.088   0.373   1178
  Planarity :  0.007   0.083   1249
  Dihedral  : 15.201  89.233   2486
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.93 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.17 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.66 (0.22), residues: 933
  helix: -2.92 (0.19), residues: 421
  sheet: -2.74 (0.41), residues: 128
  loop : -3.25 (0.26), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.002   TRP G 121 
   HIS   0.006   0.001   HIS G 149 
   PHE   0.016   0.002   PHE F 761 
   TYR   0.016   0.002   TYR G 130 
   ARG   0.006   0.000   ARG F 754 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.904 
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
  outliers start: 22
  outliers final: 7
  residues processed: 149
  average time/residue: 0.2060
  time to fit residues: 40.3127
Evaluate side-chains
  78 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.1454
  time to fit residues: 2.5475
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
F  74 ASN
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 144 GLN
F 268 HIS
F 395 ASN
F 738 ASN
F 782 ASN
F 849 GLN
F 859 ASN
F 868 HIS
G 147 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7157  Z= 0.239
  Angle     :  0.739  11.083   9772  Z= 0.363
  Chirality :  0.043   0.151   1178
  Planarity :  0.005   0.064   1249
  Dihedral  :  5.234  23.236   1017
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.07 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 21.10 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.25), residues: 933
  helix: -0.93 (0.23), residues: 446
  sheet: -1.87 (0.46), residues: 125
  loop : -3.08 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP F 802 
   HIS   0.004   0.001   HIS F 137 
   PHE   0.018   0.002   PHE G 140 
   TYR   0.015   0.002   TYR G 130 
   ARG   0.009   0.001   ARG F 340 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1363
  time to fit residues: 19.7919
Evaluate side-chains
  72 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.891 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 12
  outliers final: 1
  residues processed: 12
  average time/residue: 0.0770
  time to fit residues: 2.8005
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 84 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0870
   overall best weight:    1.6178

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 137 HIS
F 286 GLN
** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7157  Z= 0.197
  Angle     :  0.725  13.645   9772  Z= 0.339
  Chirality :  0.042   0.158   1178
  Planarity :  0.004   0.052   1249
  Dihedral  :  4.649  20.501   1017
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.75 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 23.27 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.27), residues: 933
  helix: -0.13 (0.24), residues: 462
  sheet: -1.67 (0.48), residues: 129
  loop : -2.66 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP F 326 
   HIS   0.003   0.001   HIS F 555 
   PHE   0.011   0.001   PHE G 140 
   TYR   0.008   0.001   TYR F 716 
   ARG   0.005   0.000   ARG G 106 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 7
  residues processed: 85
  average time/residue: 0.1554
  time to fit residues: 19.1552
Evaluate side-chains
  66 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.811 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.1128
  time to fit residues: 2.2910
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 89 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.5169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7157  Z= 0.144
  Angle     :  0.668  14.570   9772  Z= 0.304
  Chirality :  0.041   0.156   1178
  Planarity :  0.004   0.051   1249
  Dihedral  :  4.202  18.504   1017
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.65 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 23.12 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.27), residues: 933
  helix:  0.34 (0.24), residues: 464
  sheet: -1.22 (0.49), residues: 125
  loop : -2.43 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP F 381 
   HIS   0.003   0.000   HIS F 555 
   PHE   0.008   0.001   PHE F 171 
   TYR   0.008   0.001   TYR F 716 
   ARG   0.004   0.000   ARG G 106 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1492
  time to fit residues: 16.9704
Evaluate side-chains
  61 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.849 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0762
  time to fit residues: 1.2987
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 74 optimal weight:    0.0670
   chunk 51 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7157  Z= 0.135
  Angle     :  0.658  10.388   9772  Z= 0.295
  Chirality :  0.041   0.164   1178
  Planarity :  0.004   0.052   1249
  Dihedral  :  3.968  17.906   1017
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 23.99 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.28), residues: 933
  helix:  0.56 (0.25), residues: 465
  sheet: -1.13 (0.50), residues: 123
  loop : -2.25 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 381 
   HIS   0.002   0.000   HIS F 555 
   PHE   0.008   0.001   PHE F 431 
   TYR   0.007   0.001   TYR F 301 
   ARG   0.004   0.000   ARG F 342 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 2
  residues processed: 79
  average time/residue: 0.1316
  time to fit residues: 16.0010
Evaluate side-chains
  64 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.876 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0660
  time to fit residues: 1.3798
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0040
   chunk 22 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 571 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.5900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7157  Z= 0.140
  Angle     :  0.645  11.743   9772  Z= 0.291
  Chirality :  0.042   0.335   1178
  Planarity :  0.004   0.053   1249
  Dihedral  :  3.923  17.332   1017
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 25.29 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.28), residues: 933
  helix:  0.67 (0.25), residues: 472
  sheet: -1.15 (0.49), residues: 125
  loop : -2.10 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP G 121 
   HIS   0.003   0.000   HIS F 555 
   PHE   0.008   0.001   PHE F  72 
   TYR   0.009   0.001   TYR F 564 
   ARG   0.005   0.000   ARG G 117 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 68
  average time/residue: 0.1343
  time to fit residues: 14.0506
Evaluate side-chains
  61 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.849 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0633
  time to fit residues: 1.1410
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 89 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
F  47 HIS
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.6336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7157  Z= 0.169
  Angle     :  0.653  11.114   9772  Z= 0.301
  Chirality :  0.042   0.305   1178
  Planarity :  0.004   0.054   1249
  Dihedral  :  3.944  17.692   1017
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 25.87 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.29), residues: 933
  helix:  0.87 (0.25), residues: 471
  sheet: -1.33 (0.48), residues: 118
  loop : -1.90 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP F 802 
   HIS   0.003   0.001   HIS F 555 
   PHE   0.011   0.001   PHE F 171 
   TYR   0.011   0.001   TYR F  71 
   ARG   0.002   0.000   ARG F 750 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 74
  average time/residue: 0.1402
  time to fit residues: 15.9156
Evaluate side-chains
  60 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.855 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0648
  time to fit residues: 1.4296
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0470
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 56 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0070
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.3100

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.6695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7157  Z= 0.166
  Angle     :  0.665  11.567   9772  Z= 0.302
  Chirality :  0.042   0.337   1178
  Planarity :  0.004   0.051   1249
  Dihedral  :  3.923  17.430   1017
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.32 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 26.59 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.29), residues: 933
  helix:  1.03 (0.25), residues: 468
  sheet: -1.22 (0.48), residues: 118
  loop : -1.85 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP F 326 
   HIS   0.003   0.001   HIS F 555 
   PHE   0.020   0.001   PHE G 115 
   TYR   0.017   0.001   TYR F  71 
   ARG   0.002   0.000   ARG G 117 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 63
  average time/residue: 0.1452
  time to fit residues: 14.1558
Evaluate side-chains
  57 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0639
  time to fit residues: 1.4513
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 85 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0370
   chunk 79 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.6894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7157  Z= 0.149
  Angle     :  0.703  18.229   9772  Z= 0.311
  Chirality :  0.042   0.269   1178
  Planarity :  0.004   0.052   1249
  Dihedral  :  3.868  16.735   1017
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.89 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 27.60 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.29), residues: 933
  helix:  1.01 (0.25), residues: 474
  sheet: -1.11 (0.48), residues: 116
  loop : -1.78 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP F 381 
   HIS   0.003   0.000   HIS F 555 
   PHE   0.026   0.001   PHE G 115 
   TYR   0.013   0.001   TYR F 564 
   ARG   0.002   0.000   ARG F 624 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 58
  average time/residue: 0.1541
  time to fit residues: 13.9053
Evaluate side-chains
  56 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.779 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0702
  time to fit residues: 1.1546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 92 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0000
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.7050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7157  Z= 0.145
  Angle     :  0.708  16.854   9772  Z= 0.309
  Chirality :  0.042   0.299   1178
  Planarity :  0.004   0.060   1249
  Dihedral  :  3.824  17.042   1017
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.93 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 27.17 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.29), residues: 933
  helix:  1.02 (0.25), residues: 478
  sheet: -1.05 (0.48), residues: 118
  loop : -1.80 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.033   0.002   TRP F 326 
   HIS   0.003   0.000   HIS F 555 
   PHE   0.005   0.001   PHE F 587 
   TYR   0.011   0.001   TYR F  71 
   ARG   0.002   0.000   ARG G 117 

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 61
  average time/residue: 0.1353
  time to fit residues: 12.8084
Evaluate side-chains
  57 residues out of total 840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.778 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0640
  time to fit residues: 1.2391
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    0.0670
   chunk 68 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.037088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.027942 restraints weight = 56518.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.028768 restraints weight = 36444.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.029371 restraints weight = 26743.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.7198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7157  Z= 0.143
  Angle     :  0.714  16.269   9772  Z= 0.313
  Chirality :  0.042   0.262   1178
  Planarity :  0.004   0.056   1249
  Dihedral  :  3.795  16.545   1017
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.89 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.46 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.29), residues: 933
  helix:  1.04 (0.25), residues: 475
  sheet: -0.98 (0.48), residues: 118
  loop : -1.67 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.069   0.003   TRP F 326 
   HIS   0.003   0.000   HIS F 555 
   PHE   0.033   0.001   PHE G 115 
   TYR   0.012   0.001   TYR F 301 
   ARG   0.002   0.000   ARG F 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1492.13 seconds
wall clock time: 27 minutes 48.20 seconds (1668.20 seconds total)