Starting phenix.real_space_refine
on Tue Nov 14 20:14:24 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/11_2023/5uar_8461_updated.pdb"
  }
  resolution = 3.73
  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=   0.013 sd=   0.196
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      55      5.16       5
     C    6177      2.51       5
     N    1585      2.21       5
     O    1672      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG    3": "NH1" <-> "NH2"
    Residue "A ARG   14": "NH1" <-> "NH2"
    Residue "A ARG   52": "NH1" <-> "NH2"
    Residue "A ARG  135": "NH1" <-> "NH2"
    Residue "A ARG  154": "NH1" <-> "NH2"
    Residue "A ARG  171": "NH1" <-> "NH2"
    Residue "A ARG  259": "NH1" <-> "NH2"
    Residue "A ARG  298": "NH1" <-> "NH2"
    Residue "A ARG  330": "NH1" <-> "NH2"
    Residue "A ARG  348": "NH1" <-> "NH2"
    Residue "A ARG  482": "NH1" <-> "NH2"
    Residue "A ARG  667": "NH1" <-> "NH2"
    Residue "A ARG  849": "NH1" <-> "NH2"
    Residue "A PHE  863": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  888": "NH1" <-> "NH2"
    Residue "A ARG  979": "NH1" <-> "NH2"
    Residue "A ARG 1038": "NH1" <-> "NH2"
    Residue "A ARG 1043": "NH1" <-> "NH2"
    Residue "A ARG 1078": "NH1" <-> "NH2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 9489
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1186, 9489
          Unusual residues: {'D10': 2}
          Classifications: {'peptide': 1184, 'undetermined': 2}
          Link IDs: {'PTRANS': 39, 'TRANS': 1144, None: 2}
            Not linked:
              pdbres="HIS A1437 "
              pdbres="D10 A1501 "
            Not linked:
              pdbres="D10 A1501 "
              pdbres="D10 A1502 "
          Chain breaks: 4
  Time building chain proxies: 5.52, per 1000 atoms: 0.58
  Number of scatterers: 9489
  At special positions: 0
  Unit cell: (105, 122.64, 121.8, 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      55     16.00
     O    1672      8.00
     N    1585      7.00
     C    6177      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: 3.57
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2234

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      50 helices and 2 sheets defined
      62.0% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 8
    Processing helix  chain 'A' and resid 11 through 16
    Processing helix  chain 'A' and resid 21 through 29
      removed outlier: 3.541A  pdb=" N   GLY A  27 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A  28 " --> pdb=" O   MET A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 62
      removed outlier: 3.623A  pdb=" N   ARG A  52 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 77
      removed outlier: 3.501A  pdb=" N   ARG A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   CYS A  77 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 109
      removed outlier: 3.884A  pdb=" N   LEU A  84 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   LEU A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TYR A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   LYS A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   THR A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      Proline residue:  A 100  - end of helix
      removed outlier: 3.784A  pdb=" N   ILE A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 165
      removed outlier: 3.753A  pdb=" N   ALA A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE A 136 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
      removed outlier: 3.732A  pdb=" N   HIS A 147 " --> pdb=" O   MET A 143 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA A 156 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 174
      removed outlier: 4.065A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 170 through 174'
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.086A  pdb=" N   MET A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 215
      removed outlier: 4.103A  pdb=" N   ASP A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLN A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLY A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   MET A 198 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ALA A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   HIS A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   PHE A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ILE A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   TRP A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.583A  pdb=" N   LEU A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 268
      removed outlier: 3.560A  pdb=" N   ILE A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS A 244 " --> pdb=" O   PHE A 240 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      Proline residue:  A 247  - end of helix
      removed outlier: 3.735A  pdb=" N   GLN A 251 " --> pdb=" O   PRO A 247 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASN A 257 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 281 through 327
      removed outlier: 3.630A  pdb=" N   ILE A 286 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ASP A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLU A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   PHE A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   TYR A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   TYR A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   PHE A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA A 315 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   ILE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      Proline residue:  A 325  - end of helix
    Processing helix  chain 'A' and resid 334 through 352
      removed outlier: 3.764A  pdb=" N   THR A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU A 347 " --> pdb=" O   TYR A 343 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 376
      removed outlier: 3.544A  pdb=" N   MET A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASP A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 366 " --> pdb=" O   TRP A 362 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS A 371 " --> pdb=" O   ARG A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.610A  pdb=" N   ILE A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 506
    Processing helix  chain 'A' and resid 514 through 522
    Processing helix  chain 'A' and resid 526 through 531
      removed outlier: 3.564A  pdb=" N   ALA A 530 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 537
      No H-bonds generated for 'chain 'A' and resid 535 through 537'
    Processing helix  chain 'A' and resid 549 through 562
      removed outlier: 3.781A  pdb=" N   ARG A 559 " --> pdb=" O   VAL A 555 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ALA A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 592
      removed outlier: 3.745A  pdb=" N   LYS A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU A 590 " --> pdb=" O   PHE A 586 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   CYS A 591 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS A 592 " --> pdb=" O   LYS A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 596
      No H-bonds generated for 'chain 'A' and resid 594 through 596'
    Processing helix  chain 'A' and resid 606 through 611
    Processing helix  chain 'A' and resid 629 through 634
      removed outlier: 3.567A  pdb=" N   SER A 634 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 644
    Processing helix  chain 'A' and resid 654 through 668
      removed outlier: 3.718A  pdb=" N   HIS A 666 " --> pdb=" O   THR A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 856 through 881
      removed outlier: 3.710A  pdb=" N   LEU A 861 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   PHE A 863 " --> pdb=" O   TYR A 859 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 864 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE A 866 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ALA A 868 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 890
      removed outlier: 4.102A  pdb=" N   GLU A 890 " --> pdb=" O   LEU A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 929
      removed outlier: 3.715A  pdb=" N   ALA A 929 " --> pdb=" O   TYR A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 934
      No H-bonds generated for 'chain 'A' and resid 931 through 934'
    Processing helix  chain 'A' and resid 939 through 965
      Proline residue:  A 944  - end of helix
      removed outlier: 3.578A  pdb=" N   HIS A 947 " --> pdb=" O   LEU A 943 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR A 951 " --> pdb=" O   HIS A 947 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE A 952 " --> pdb=" O   THR A 948 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 953 " --> pdb=" O   THR A 949 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN A 958 " --> pdb=" O   LYS A 954 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   MET A 960 " --> pdb=" O   LEU A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 985
      removed outlier: 3.699A  pdb=" N   PHE A 984 " --> pdb=" O   ILE A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 992
    Processing helix  chain 'A' and resid 994 through 1019
      removed outlier: 3.546A  pdb=" N   LEU A 998 " --> pdb=" O   MET A 994 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A1000 " --> pdb=" O   PRO A 996 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP A1001 " --> pdb=" O   LEU A 997 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   PHE A1002 " --> pdb=" O   LEU A 998 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A1006 " --> pdb=" O   PHE A1002 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A1007 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   VAL A1015 " --> pdb=" O   GLY A1011 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   VAL A1019 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1068
      removed outlier: 4.204A  pdb=" N   THR A1028 " --> pdb=" O   LEU A1025 " (cutoff:3.500A)
      Proline residue:  A1029  - end of helix
      removed outlier: 3.546A  pdb=" N   ILE A1033 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ILE A1035 " --> pdb=" O   ILE A1032 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET A1037 " --> pdb=" O   PHE A1034 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A1042 " --> pdb=" O   LYS A1039 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ARG A1043 " --> pdb=" O   TYR A1040 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR A1044 " --> pdb=" O   PHE A1041 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   GLN A1046 " --> pdb=" O   ARG A1043 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN A1047 " --> pdb=" O   THR A1044 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS A1049 " --> pdb=" O   GLN A1046 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN A1050 " --> pdb=" O   GLN A1047 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A1051 " --> pdb=" O   LEU A1048 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU A1054 " --> pdb=" O   LEU A1051 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG A1056 " --> pdb=" O   THR A1053 " (cutoff:3.500A)
      Proline residue:  A1058  - end of helix
      removed outlier: 3.841A  pdb=" N   HIS A1062 " --> pdb=" O   ILE A1059 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A1064 " --> pdb=" O   SER A1061 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   MET A1065 " --> pdb=" O   HIS A1062 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LYS A1068 " --> pdb=" O   MET A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1075
      removed outlier: 3.920A  pdb=" N   ARG A1074 " --> pdb=" O   LEU A1070 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A1075 " --> pdb=" O   TRP A1071 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1070 through 1075'
    Processing helix  chain 'A' and resid 1079 through 1127
      removed outlier: 3.729A  pdb=" N   HIS A1087 " --> pdb=" O   GLU A1083 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS A1088 " --> pdb=" O   ALA A1084 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A1089 " --> pdb=" O   LEU A1085 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A1090 " --> pdb=" O   PHE A1086 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS A1093 " --> pdb=" O   THR A1089 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A1115 " --> pdb=" O   ALA A1111 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL A1116 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A1117 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A1118 " --> pdb=" O   LEU A1114 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL A1127 " --> pdb=" O   ALA A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1175
      removed outlier: 3.719A  pdb=" N   CYS A1142 " --> pdb=" O   GLY A1138 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A1146 " --> pdb=" O   CYS A1142 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ILE A1147 " --> pdb=" O   LEU A1143 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LEU A1148 " --> pdb=" O   ALA A1144 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   GLY A1149 " --> pdb=" O   MET A1145 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   THR A1150 " --> pdb=" O   LEU A1146 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TRP A1153 " --> pdb=" O   GLY A1149 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE A1159 " --> pdb=" O   VAL A1155 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA A1160 " --> pdb=" O   ALA A1156 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A1162 " --> pdb=" O   SER A1158 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG A1166 " --> pdb=" O   ASP A1162 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   SER A1167 " --> pdb=" O   GLY A1163 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A1168 " --> pdb=" O   MET A1164 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP A1169 " --> pdb=" O   MET A1165 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ARG A1170 " --> pdb=" O   ARG A1166 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A1171 " --> pdb=" O   SER A1167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1251 through 1259
      removed outlier: 4.175A  pdb=" N   PHE A1255 " --> pdb=" O   LYS A1251 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A1258 " --> pdb=" O   LEU A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1280 through 1284
    Processing helix  chain 'A' and resid 1301 through 1305
    Processing helix  chain 'A' and resid 1313 through 1323
    Processing helix  chain 'A' and resid 1327 through 1330
      No H-bonds generated for 'chain 'A' and resid 1327 through 1330'
    Processing helix  chain 'A' and resid 1351 through 1363
      removed outlier: 4.217A  pdb=" N   CYS A1356 " --> pdb=" O   LYS A1352 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A1361 " --> pdb=" O   LEU A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1374 through 1376
      No H-bonds generated for 'chain 'A' and resid 1374 through 1376'
    Processing helix  chain 'A' and resid 1379 through 1392
      removed outlier: 3.764A  pdb=" N   LYS A1383 " --> pdb=" O   PRO A1379 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL A1384 " --> pdb=" O   VAL A1380 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A1389 " --> pdb=" O   LEU A1385 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG A1390 " --> pdb=" O   LYS A1386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1406 through 1409
    Processing helix  chain 'A' and resid 1428 through 1431
      No H-bonds generated for 'chain 'A' and resid 1428 through 1431'
    Processing sheet with id=  A, first strand: chain 'A' and resid 599 through 601
      removed outlier: 6.350A  pdb=" N   LYS A 614 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   THR A 456 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   LEU A 616 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   HIS A 619 " --> pdb=" O   SER A 623 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   SER A 623 " --> pdb=" O   HIS A 619 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 1413 through 1416
      removed outlier: 4.228A  pdb=" N   SER A1413 " --> pdb=" O   ARG A1240 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ILE A1398 " --> pdb=" O   VAL A1241 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   ILE A1243 " --> pdb=" O   ILE A1398 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU A1400 " --> pdb=" O   ILE A1243 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A1401 " --> pdb=" O   LEU A1370 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1044 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: 2.87

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2933
        1.35 -     1.48: 2373
        1.48 -     1.61: 4295
        1.61 -     1.73: 0
        1.73 -     1.86: 93
  Bond restraints: 9694
  Sorted by residual:
  bond pdb=" CA  ILE A 337 "
       pdb=" CB  ILE A 337 "
    ideal  model  delta    sigma   weight residual
    1.539  1.576 -0.037 1.13e-02 7.83e+03 1.06e+01
  bond pdb=" N   LEU A 995 "
       pdb=" CA  LEU A 995 "
    ideal  model  delta    sigma   weight residual
    1.463  1.482 -0.018 6.90e-03 2.10e+04 7.09e+00
  bond pdb=" CA  ARG A1020 "
       pdb=" C   ARG A1020 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.026 1.00e-02 1.00e+04 6.53e+00
  bond pdb=" N   LEU A 189 "
       pdb=" CA  LEU A 189 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.16e-02 7.43e+03 6.36e+00
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.504 -0.046 1.90e-02 2.77e+03 5.78e+00
  ... (remaining 9689 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   107.08: 239
      107.08 -   113.83: 5283
      113.83 -   120.58: 3956
      120.58 -   127.34: 3524
      127.34 -   134.09: 93
  Bond angle restraints: 13095
  Sorted by residual:
  angle pdb=" N   MET A 975 "
        pdb=" CA  MET A 975 "
        pdb=" C   MET A 975 "
      ideal   model   delta    sigma   weight residual
     111.28  116.93   -5.65 1.09e+00 8.42e-01 2.69e+01
  angle pdb=" N   ASN A 188 "
        pdb=" CA  ASN A 188 "
        pdb=" C   ASN A 188 "
      ideal   model   delta    sigma   weight residual
     112.23  118.67   -6.44 1.26e+00 6.30e-01 2.61e+01
  angle pdb=" C   ASP A1378 "
        pdb=" N   PRO A1379 "
        pdb=" CA  PRO A1379 "
      ideal   model   delta    sigma   weight residual
     119.84  125.15   -5.31 1.25e+00 6.40e-01 1.80e+01
  angle pdb=" N   PHE A 110 "
        pdb=" CA  PHE A 110 "
        pdb=" C   PHE A 110 "
      ideal   model   delta    sigma   weight residual
     108.52  115.42   -6.90 1.63e+00 3.76e-01 1.79e+01
  angle pdb=" N   GLN A  39 "
        pdb=" CA  GLN A  39 "
        pdb=" C   GLN A  39 "
      ideal   model   delta    sigma   weight residual
     110.33  115.69   -5.36 1.29e+00 6.01e-01 1.73e+01
  ... (remaining 13090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5328
       17.79 -    35.59: 385
       35.59 -    53.38: 83
       53.38 -    71.17: 12
       71.17 -    88.97: 2
  Dihedral angle restraints: 5810
    sinusoidal: 2357
      harmonic: 3453
  Sorted by residual:
  dihedral pdb=" CA  CYS A  77 "
           pdb=" C   CYS A  77 "
           pdb=" N   TYR A  78 "
           pdb=" CA  TYR A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.30   23.70     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  ASP A 174 "
           pdb=" C   ASP A 174 "
           pdb=" N   LYS A 175 "
           pdb=" CA  LYS A 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.99   19.01     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ARG A1284 "
           pdb=" C   ARG A1284 "
           pdb=" N   LYS A1285 "
           pdb=" CA  LYS A1285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.50   17.50     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 5807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1027
       0.054 -    0.107: 352
       0.107 -    0.161: 97
       0.161 -    0.215: 22
       0.215 -    0.268: 5
  Chirality restraints: 1503
  Sorted by residual:
  chirality pdb=" CA  THR A 977 "
            pdb=" N   THR A 977 "
            pdb=" C   THR A 977 "
            pdb=" CB  THR A 977 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  PHE A 201 "
            pdb=" N   PHE A 201 "
            pdb=" C   PHE A 201 "
            pdb=" CB  PHE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  ILE A1296 "
            pdb=" N   ILE A1296 "
            pdb=" C   ILE A1296 "
            pdb=" CB  ILE A1296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1500 not shown)

  Planarity restraints: 1611
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  99 "   -0.035 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO A 100 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 100 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 100 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1057 "   -0.033 5.00e-02 4.00e+02   5.05e-02 4.07e+00
        pdb=" N   PRO A1058 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A1058 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1058 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 324 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A 325 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1608 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3219
        2.89 -     3.40: 9476
        3.40 -     3.90: 14378
        3.90 -     4.40: 15323
        4.40 -     4.90: 26561
  Nonbonded interactions: 68957
  Sorted by model distance:
  nonbonded pdb=" O   VAL A1384 "
            pdb=" OG1 THR A1388 "
     model   vdw
     2.393 2.440
  nonbonded pdb=" O   TYR A1220 "
            pdb=" OG1 THR A1221 "
     model   vdw
     2.508 2.440
  nonbonded pdb=" O   ASN A  10 "
            pdb=" OG  SER A  13 "
     model   vdw
     2.539 2.440
  nonbonded pdb=" O   GLU A 293 "
            pdb=" OG1 THR A 297 "
     model   vdw
     2.558 2.440
  nonbonded pdb=" O   PHE A 945 "
            pdb=" OG1 THR A 949 "
     model   vdw
     2.564 2.440
  ... (remaining 68952 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=0.65 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:             1.900
  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:          7.430
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     28.270
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.008   0.054   9694  Z= 0.505
  Angle     :  1.182   8.467  13095  Z= 0.816
  Chirality :  0.061   0.268   1503
  Planarity :  0.004   0.053   1611
  Dihedral  : 13.303  88.968   3576
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 0.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.41 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  5.89 %
    Favored  : 93.04 %
  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: -3.58 (0.20), residues: 1174
  helix: -2.16 (0.15), residues: 702
  sheet: -2.76 (0.65), residues: 33
  loop : -2.46 (0.28), residues: 439

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 350
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 358
  average time/residue: 0.2316
  time to fit residues: 112.5440
Evaluate side-chains
  221 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 1.099 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0899
  time to fit residues: 1.7060
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0870
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0670
   overall best weight:    1.4302

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

Flipped N/Q/H residues before XYZ refinement:
A 396 GLN
A 620 ASN
** A1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9694  Z= 0.226
  Angle     :  0.662   8.577  13095  Z= 0.337
  Chirality :  0.042   0.159   1503
  Planarity :  0.004   0.042   1611
  Dihedral  :  5.053  17.641   1295
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.46 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.49 (0.23), residues: 1174
  helix: -0.26 (0.18), residues: 717
  sheet: -2.29 (0.59), residues: 52
  loop : -2.01 (0.30), residues: 405

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 239
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 41
  outliers final: 20
  residues processed: 259
  average time/residue: 0.1979
  time to fit residues: 73.0292
Evaluate side-chains
  225 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 1.094 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0900
  time to fit residues: 4.8579
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 106 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 238 GLN
** A1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9694  Z= 0.171
  Angle     :  0.611   9.591  13095  Z= 0.303
  Chirality :  0.039   0.166   1503
  Planarity :  0.004   0.046   1611
  Dihedral  :  4.748  19.408   1295
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.23 %
    Favored  : 78.16 %
  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: -0.82 (0.24), residues: 1174
  helix:  0.33 (0.19), residues: 697
  sheet: -1.66 (0.59), residues: 55
  loop : -1.81 (0.30), residues: 422

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 17
  residues processed: 242
  average time/residue: 0.2026
  time to fit residues: 69.4184
Evaluate side-chains
  214 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 1.023 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0943
  time to fit residues: 4.4090
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0770
   chunk 114 optimal weight:    7.9990
   chunk 56 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A1131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9694  Z= 0.168
  Angle     :  0.594   9.719  13095  Z= 0.291
  Chirality :  0.039   0.163   1503
  Planarity :  0.004   0.077   1611
  Dihedral  :  4.576  18.200   1295
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.39 %
    Favored  : 77.29 %
  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: -0.53 (0.24), residues: 1174
  helix:  0.54 (0.19), residues: 697
  sheet: -1.04 (0.62), residues: 50
  loop : -1.72 (0.29), residues: 427

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 220
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 12
  residues processed: 234
  average time/residue: 0.1972
  time to fit residues: 65.9097
Evaluate side-chains
  213 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 1.048 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0929
  time to fit residues: 3.4551
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0170
   chunk 78 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.1424

-------------------------------------------------------------------------------
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: 0.7728
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9694  Z= 0.184
  Angle     :  0.580   7.015  13095  Z= 0.286
  Chirality :  0.039   0.167   1503
  Planarity :  0.004   0.057   1611
  Dihedral  :  4.520  20.189   1295
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.22 %
    Favored  : 75.75 %
  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 (0.24), residues: 1174
  helix:  0.63 (0.19), residues: 698
  sheet: -0.68 (0.66), residues: 43
  loop : -1.71 (0.28), residues: 433

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 9
  residues processed: 226
  average time/residue: 0.2015
  time to fit residues: 65.0705
Evaluate side-chains
  207 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 198
  time to evaluate  : 1.081 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0872
  time to fit residues: 3.0548
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 114 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0020
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    8.9990
   overall best weight:    1.0592

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

Flipped N/Q/H residues before XYZ refinement:
A 957 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9694  Z= 0.182
  Angle     :  0.609   9.571  13095  Z= 0.297
  Chirality :  0.039   0.171   1503
  Planarity :  0.004   0.057   1611
  Dihedral  :  4.510  22.892   1295
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.57 %
    Favored  : 74.30 %
  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: -0.38 (0.24), residues: 1174
  helix:  0.65 (0.19), residues: 690
  sheet: -0.80 (0.63), residues: 55
  loop : -1.63 (0.28), residues: 429

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 11
  residues processed: 231
  average time/residue: 0.1936
  time to fit residues: 64.7483
Evaluate side-chains
  211 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 1.122 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0941
  time to fit residues: 3.4125
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0770
   chunk 71 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.8542

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.5500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9694  Z= 0.172
  Angle     :  0.619  10.138  13095  Z= 0.299
  Chirality :  0.040   0.176   1503
  Planarity :  0.004   0.056   1611
  Dihedral  :  4.483  24.130   1295
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 24.44 %
    Favored  : 74.40 %
  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: -0.36 (0.24), residues: 1174
  helix:  0.60 (0.19), residues: 703
  sheet: -0.61 (0.63), residues: 55
  loop : -1.59 (0.29), residues: 416

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 209
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 214
  average time/residue: 0.1979
  time to fit residues: 60.9471
Evaluate side-chains
  206 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 199
  time to evaluate  : 1.202 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1039
  time to fit residues: 2.8833
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0870
   chunk 103 optimal weight:    0.0060
   overall best weight:    0.7376

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

Flipped N/Q/H residues before XYZ refinement:
A 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.5685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9694  Z= 0.165
  Angle     :  0.634  10.521  13095  Z= 0.303
  Chirality :  0.040   0.185   1503
  Planarity :  0.004   0.053   1611
  Dihedral  :  4.492  29.511   1295
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 25.31 %
    Favored  : 73.53 %
  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: -0.33 (0.24), residues: 1174
  helix:  0.65 (0.20), residues: 697
  sheet: -0.63 (0.63), residues: 57
  loop : -1.59 (0.29), residues: 420

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 203
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 212
  average time/residue: 0.1968
  time to fit residues: 60.3517
Evaluate side-chains
  204 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 199
  time to evaluate  : 1.138 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0945
  time to fit residues: 2.4744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0670
   chunk 100 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9694  Z= 0.196
  Angle     :  0.654   9.975  13095  Z= 0.311
  Chirality :  0.040   0.175   1503
  Planarity :  0.004   0.054   1611
  Dihedral  :  4.547  31.090   1295
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 25.60 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.33 (0.24), residues: 1174
  helix:  0.63 (0.19), residues: 705
  sheet: -0.55 (0.65), residues: 57
  loop : -1.61 (0.29), residues: 412

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 8
  residues processed: 208
  average time/residue: 0.1980
  time to fit residues: 59.7334
Evaluate side-chains
  202 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 194
  time to evaluate  : 1.245 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1058
  time to fit residues: 3.1996
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0370
   chunk 77 optimal weight:    0.9980
   chunk 117 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 GLN
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.5942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9694  Z= 0.169
  Angle     :  0.657   9.262  13095  Z= 0.312
  Chirality :  0.040   0.176   1503
  Planarity :  0.004   0.055   1611
  Dihedral  :  4.492  30.662   1295
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 26.18 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.32 (0.24), residues: 1174
  helix:  0.67 (0.20), residues: 699
  sheet: -0.44 (0.65), residues: 57
  loop : -1.65 (0.28), residues: 418

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 212
  average time/residue: 0.2065
  time to fit residues: 62.8280
Evaluate side-chains
  201 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 1.066 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0891
  time to fit residues: 1.6442
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 96 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.122938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.100859 restraints weight = 24906.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.103941 restraints weight = 12927.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.105957 restraints weight = 8270.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.6034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9694  Z= 0.164
  Angle     :  0.643   9.255  13095  Z= 0.304
  Chirality :  0.039   0.185   1503
  Planarity :  0.004   0.054   1611
  Dihedral  :  4.428  30.008   1295
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 26.86 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.29 (0.24), residues: 1174
  helix:  0.69 (0.20), residues: 698
  sheet: -0.48 (0.65), residues: 58
  loop : -1.63 (0.28), residues: 418
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2322.50 seconds
wall clock time: 42 minutes 58.91 seconds (2578.91 seconds total)