Starting phenix.real_space_refine
on Sat Mar 16 11:40:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_ligands.cif

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty9_20582/03_2024/6ty9_20582_updated.pdb"
  }
  resolution = 2.9
  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=   0.009
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: 6
    Type Number    sf(0)   Gaussians
     P      44      5.49       5
     Mg      3      5.21       5
     S      54      5.16       5
     C    9100      2.51       5
     N    2482      2.21       5
     O    2876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  117": "OE1" <-> "OE2"
    Residue "A ARG  147": "NH1" <-> "NH2"
    Residue "A GLU  180": "OE1" <-> "OE2"
    Residue "A GLU  245": "OE1" <-> "OE2"
    Residue "A GLU  313": "OE1" <-> "OE2"
    Residue "A ARG  317": "NH1" <-> "NH2"
    Residue "A GLU  434": "OE1" <-> "OE2"
    Residue "A GLU  437": "OE1" <-> "OE2"
    Residue "A ARG  465": "NH1" <-> "NH2"
    Residue "A ARG  484": "NH1" <-> "NH2"
    Residue "A ARG  485": "NH1" <-> "NH2"
    Residue "A ARG  487": "NH1" <-> "NH2"
    Residue "A ARG  578": "NH1" <-> "NH2"
    Residue "A GLU  625": "OE1" <-> "OE2"
    Residue "A GLU  634": "OE1" <-> "OE2"
    Residue "A ARG  641": "NH1" <-> "NH2"
    Residue "A GLU  690": "OE1" <-> "OE2"
    Residue "A GLU  714": "OE1" <-> "OE2"
    Residue "A ARG  738": "NH1" <-> "NH2"
    Residue "A ARG  752": "NH1" <-> "NH2"
    Residue "A ARG  841": "NH1" <-> "NH2"
    Residue "A GLU  859": "OE1" <-> "OE2"
    Residue "A ARG  867": "NH1" <-> "NH2"
    Residue "A ARG  872": "NH1" <-> "NH2"
    Residue "A ARG  882": "NH1" <-> "NH2"
    Residue "A GLU  899": "OE1" <-> "OE2"
    Residue "A GLU  947": "OE1" <-> "OE2"
    Residue "A ARG  950": "NH1" <-> "NH2"
    Residue "A ARG  951": "NH1" <-> "NH2"
    Residue "A GLU  975": "OE1" <-> "OE2"
    Residue "A ARG  993": "NH1" <-> "NH2"
    Residue "A ARG  997": "NH1" <-> "NH2"
    Residue "A ARG 1007": "NH1" <-> "NH2"
    Residue "A GLU 1025": "OE1" <-> "OE2"
    Residue "A GLU 1120": "OE1" <-> "OE2"
    Residue "A ARG 1146": "NH1" <-> "NH2"
    Residue "B PHE    2": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   71": "NH1" <-> "NH2"
    Residue "B GLU  146": "OE1" <-> "OE2"
    Residue "B ARG  199": "NH1" <-> "NH2"
    Residue "B GLU  337": "OE1" <-> "OE2"
    Residue "B GLU  433": "OE1" <-> "OE2"
    Residue "B ARG  520": "NH1" <-> "NH2"
    Residue "B GLU  552": "OE1" <-> "OE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 14559
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1208, 9667
          Classifications: {'peptide': 1208}
          Link IDs: {'PTRANS': 38, 'TRANS': 1169}
    Chain: "B"
      Number of atoms: 4007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 4007
          Classifications: {'peptide': 501}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482}
          Chain breaks: 2
    Chain: "M"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 1}
          Link IDs: {None: 1}
    Chain: "N"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 418
          Unusual residues: {'GTA': 1}
          Classifications: {'RNA': 18, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 15}
          Link IDs: {'rna3p': 17, None: 1}
            Not linked:
              pdbres="GTA N   1 "
              pdbres="  G N   2 "
    Chain: "T"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 410
          Classifications: {'RNA': 19}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 16}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.38, per 1000 atoms: 0.58
  Number of scatterers: 14559
  At special positions: 0
  Unit cell: (105.138, 143.37, 106.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P      44     15.00
     Mg      3     11.99
     O    2876      8.00
     N    2482      7.00
     C    9100      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 5.61
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3234

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      82 helices and 14 sheets defined
      45.5% alpha, 8.3% beta
      9 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 6.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 9
      No H-bonds generated for 'chain 'A' and resid 7 through 9'
    Processing helix  chain 'A' and resid 12 through 15
      No H-bonds generated for 'chain 'A' and resid 12 through 15'
    Processing helix  chain 'A' and resid 22 through 35
      removed outlier: 3.622A  pdb=" N   LEU A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 44
    Processing helix  chain 'A' and resid 73 through 76
      No H-bonds generated for 'chain 'A' and resid 73 through 76'
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 109 through 111
      No H-bonds generated for 'chain 'A' and resid 109 through 111'
    Processing helix  chain 'A' and resid 121 through 134
      removed outlier: 3.619A  pdb=" N   LYS A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 160
    Processing helix  chain 'A' and resid 166 through 175
    Processing helix  chain 'A' and resid 203 through 218
      removed outlier: 3.510A  pdb=" N   VAL A 207 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   TYR A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 239
      removed outlier: 3.671A  pdb=" N   ILE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A 229 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 249
      removed outlier: 3.602A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 295 through 306
      removed outlier: 3.576A  pdb=" N   GLU A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.579A  pdb=" N   TYR A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 339
    Processing helix  chain 'A' and resid 353 through 357
    Processing helix  chain 'A' and resid 389 through 399
      removed outlier: 3.957A  pdb=" N   TYR A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   SER A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 413 through 420
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 440 through 445
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 463 through 467
    Processing helix  chain 'A' and resid 496 through 499
      No H-bonds generated for 'chain 'A' and resid 496 through 499'
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 3.825A  pdb=" N   GLN A 509 " --> pdb=" O   THR A 505 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ILE A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TYR A 511 " --> pdb=" O   GLY A 507 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ASP A 512 " --> pdb=" O   LYS A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 528
      No H-bonds generated for 'chain 'A' and resid 526 through 528'
    Processing helix  chain 'A' and resid 530 through 537
      removed outlier: 3.767A  pdb=" N   SER A 537 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 554
      No H-bonds generated for 'chain 'A' and resid 551 through 554'
    Processing helix  chain 'A' and resid 560 through 572
      removed outlier: 3.715A  pdb=" N   PHE A 566 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 614
    Processing helix  chain 'A' and resid 644 through 666
      removed outlier: 3.840A  pdb=" N   HIS A 648 " --> pdb=" O   THR A 644 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 661 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 705
    Processing helix  chain 'A' and resid 736 through 738
      No H-bonds generated for 'chain 'A' and resid 736 through 738'
    Processing helix  chain 'A' and resid 756 through 770
      removed outlier: 3.696A  pdb=" N   LEU A 767 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 768 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   PHE A 769 " --> pdb=" O   ASP A 765 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   ARG A 770 " --> pdb=" O   ASP A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 787
      removed outlier: 3.515A  pdb=" N   MET A 779 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 808
      removed outlier: 3.504A  pdb=" N   TYR A 801 " --> pdb=" O   ASN A 798 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   ASP A 802 " --> pdb=" O   LYS A 799 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR A 804 " --> pdb=" O   TYR A 801 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR A 805 " --> pdb=" O   ASP A 802 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN A 806 " --> pdb=" O   SER A 803 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASN A 807 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 838
    Processing helix  chain 'A' and resid 869 through 877
    Processing helix  chain 'A' and resid 881 through 887
      removed outlier: 3.534A  pdb=" N   GLN A 886 " --> pdb=" O   ARG A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 900
    Processing helix  chain 'A' and resid 902 through 911
    Processing helix  chain 'A' and resid 913 through 924
      removed outlier: 3.819A  pdb=" N   VAL A 920 " --> pdb=" O   LEU A 916 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ASP A 924 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 938
    Processing helix  chain 'A' and resid 947 through 957
    Processing helix  chain 'A' and resid 972 through 982
      removed outlier: 3.795A  pdb=" N   LYS A 976 " --> pdb=" O   GLY A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 1005
      removed outlier: 3.648A  pdb=" N   LYS A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG A 993 " --> pdb=" O   VAL A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1020
    Processing helix  chain 'A' and resid 1035 through 1037
      No H-bonds generated for 'chain 'A' and resid 1035 through 1037'
    Processing helix  chain 'A' and resid 1054 through 1062
    Processing helix  chain 'A' and resid 1067 through 1077
      removed outlier: 3.516A  pdb=" N   LEU A1072 " --> pdb=" O   SER A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1102
      removed outlier: 3.624A  pdb=" N   ILE A1099 " --> pdb=" O   GLN A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1113
      removed outlier: 4.906A  pdb=" N   ASN A1108 " --> pdb=" O   THR A1105 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A1109 " --> pdb=" O   LEU A1106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1133
      removed outlier: 3.526A  pdb=" N   TYR A1130 " --> pdb=" O   ARG A1126 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   LEU A1133 " --> pdb=" O   ALA A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1158
    Processing helix  chain 'A' and resid 1166 through 1168
      No H-bonds generated for 'chain 'A' and resid 1166 through 1168'
    Processing helix  chain 'A' and resid 1174 through 1188
      removed outlier: 3.507A  pdb=" N   HIS A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A1187 " --> pdb=" O   TYR A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1190 through 1192
      No H-bonds generated for 'chain 'A' and resid 1190 through 1192'
    Processing helix  chain 'A' and resid 1204 through 1211
    Processing helix  chain 'B' and resid 10 through 16
      removed outlier: 3.938A  pdb=" N   TYR B  16 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 62
      removed outlier: 3.533A  pdb=" N   LYS B  47 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ARG B  62 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 136 through 148
      removed outlier: 3.534A  pdb=" N   LEU B 144 " --> pdb=" O   GLU B 140 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
      removed outlier: 3.555A  pdb=" N   LEU B 167 " --> pdb=" O   LYS B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 178
      removed outlier: 3.552A  pdb=" N   LEU B 175 " --> pdb=" O   TYR B 171 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA B 177 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   TYR B 178 " --> pdb=" O   GLN B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.518A  pdb=" N   SER B 200 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 242
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 326 through 340
      removed outlier: 3.918A  pdb=" N   ALA B 338 " --> pdb=" O   LYS B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 374
      removed outlier: 4.047A  pdb=" N   THR B 365 " --> pdb=" O   SER B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 3.789A  pdb=" N   LYS B 392 " --> pdb=" O   ARG B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 408
    Processing helix  chain 'B' and resid 417 through 428
    Processing helix  chain 'B' and resid 434 through 438
    Processing helix  chain 'B' and resid 442 through 459
      removed outlier: 3.953A  pdb=" N   GLU B 451 " --> pdb=" O   LYS B 447 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU B 454 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B 455 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA B 458 " --> pdb=" O   GLU B 454 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLN B 459 " --> pdb=" O   VAL B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 476
    Processing helix  chain 'B' and resid 492 through 496
      removed outlier: 3.572A  pdb=" N   ALA B 496 " --> pdb=" O   ALA B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 518
    Processing helix  chain 'B' and resid 524 through 537
      removed outlier: 3.659A  pdb=" N   LEU B 537 " --> pdb=" O   THR B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 556
      removed outlier: 4.036A  pdb=" N   ILE B 554 " --> pdb=" O   MET B 550 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B 555 " --> pdb=" O   LEU B 551 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 54 through 58
    Processing sheet with id=  B, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=  C, first strand: chain 'A' and resid 475 through 477
      removed outlier: 3.578A  pdb=" N   LYS A 475 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 541 through 544
      removed outlier: 3.710A  pdb=" N   THR A 674 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   GLN A 687 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   LEU A 672 " --> pdb=" O   GLN A 687 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 585 through 590
    Processing sheet with id=  F, first strand: chain 'A' and resid 621 through 624
    Processing sheet with id=  G, first strand: chain 'A' and resid 791 through 797
      removed outlier: 3.920A  pdb=" N   THR A 813 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 1022 through 1026
    Processing sheet with id=  I, first strand: chain 'A' and resid 266 through 272
      removed outlier: 3.685A  pdb=" N   GLY A 280 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'A' and resid 370 through 373
      removed outlier: 6.571A  pdb=" N   LYS A 382 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 157 through 159
      removed outlier: 6.097A  pdb=" N   HIS B 182 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'B' and resid 204 through 208
    Processing sheet with id=  M, first strand: chain 'B' and resid 297 through 299
      removed outlier: 3.544A  pdb=" N   LYS B 315 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   THR B 261 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ILE B 313 " --> pdb=" O   THR B 261 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 543 through 546
      removed outlier: 4.229A  pdb=" N   THR B 543 " --> pdb=" O   THR B 504 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   VAL B 505 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL B 350 " --> pdb=" O   VAL B 505 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   LEU B 507 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TYR B 352 " --> pdb=" O   LEU B 507 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA B 353 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      18 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 4.87

  Time building geometry restraints manager: 6.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2287
        1.31 -     1.43: 4353
        1.43 -     1.56: 8124
        1.56 -     1.68: 89
        1.68 -     1.81: 96
  Bond restraints: 14949
  Sorted by residual:
  bond pdb=" C1A GTA N   1 "
       pdb=" O4A GTA N   1 "
    ideal  model  delta    sigma   weight residual
    1.591  1.290  0.301 2.00e-02 2.50e+03 2.27e+02
  bond pdb=" C2' GTP M   2 "
       pdb=" C3' GTP M   2 "
    ideal  model  delta    sigma   weight residual
    1.524  1.236  0.288 2.00e-02 2.50e+03 2.07e+02
  bond pdb=" C3B GTA N   1 "
       pdb=" C4B GTA N   1 "
    ideal  model  delta    sigma   weight residual
    1.275  1.544 -0.269 2.00e-02 2.50e+03 1.81e+02
  bond pdb=" C4B GTA N   1 "
       pdb=" O4B GTA N   1 "
    ideal  model  delta    sigma   weight residual
    1.556  1.303  0.253 2.00e-02 2.50e+03 1.61e+02
  bond pdb=" C1A GTA N   1 "
       pdb=" C2A GTA N   1 "
    ideal  model  delta    sigma   weight residual
    1.325  1.566 -0.241 2.00e-02 2.50e+03 1.45e+02
  ... (remaining 14944 not shown)

  Histogram of bond angle deviations from ideal:
       97.89 -   106.74: 546
      106.74 -   115.58: 9234
      115.58 -   124.42: 10310
      124.42 -   133.27: 325
      133.27 -   142.11: 22
  Bond angle restraints: 20437
  Sorted by residual:
  angle pdb=" N   GLY A 440 "
        pdb=" CA  GLY A 440 "
        pdb=" C   GLY A 440 "
      ideal   model   delta    sigma   weight residual
     111.34  123.76  -12.42 1.82e+00 3.02e-01 4.65e+01
  angle pdb=" C1A GTA N   1 "
        pdb=" N9  GTA N   1 "
        pdb=" C4  GTA N   1 "
      ideal   model   delta    sigma   weight residual
     114.98  135.42  -20.44 3.00e+00 1.11e-01 4.64e+01
  angle pdb=" C1A GTA N   1 "
        pdb=" N9  GTA N   1 "
        pdb=" C8  GTA N   1 "
      ideal   model   delta    sigma   weight residual
     133.44  113.65   19.79 3.00e+00 1.11e-01 4.35e+01
  angle pdb=" C1B GTA N   1 "
        pdb=" N9C GTA N   1 "
        pdb=" C4C GTA N   1 "
      ideal   model   delta    sigma   weight residual
     121.43  140.38  -18.95 3.00e+00 1.11e-01 3.99e+01
  angle pdb=" C1B GTA N   1 "
        pdb=" N9C GTA N   1 "
        pdb=" C8C GTA N   1 "
      ideal   model   delta    sigma   weight residual
     127.97  111.22   16.75 3.00e+00 1.11e-01 3.12e+01
  ... (remaining 20432 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.09: 8684
       34.09 -    68.18: 236
       68.18 -   102.27: 15
      102.27 -   136.36: 3
      136.36 -   170.45: 1
  Dihedral angle restraints: 8939
    sinusoidal: 3907
      harmonic: 5032
  Sorted by residual:
  dihedral pdb=" O2G GTP M   2 "
           pdb=" O3B GTP M   2 "
           pdb=" PG  GTP M   2 "
           pdb=" PB  GTP M   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -12.25 -170.45     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" O3A GTP M   2 "
           pdb=" O3B GTP M   2 "
           pdb=" PB  GTP M   2 "
           pdb=" PG  GTP M   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21   70.96 -127.16     1      2.00e+01 2.50e-03 3.85e+01
  dihedral pdb=" C8  GTP M   2 "
           pdb=" C1' GTP M   2 "
           pdb=" N9  GTP M   2 "
           pdb=" O4' GTP M   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    0.79  103.81     1      2.00e+01 2.50e-03 2.97e+01
  ... (remaining 8936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1577
       0.038 -    0.077: 571
       0.077 -    0.115: 130
       0.115 -    0.154: 32
       0.154 -    0.192: 4
  Chirality restraints: 2314
  Sorted by residual:
  chirality pdb=" CA  ILE A 433 "
            pdb=" N   ILE A 433 "
            pdb=" C   ILE A 433 "
            pdb=" CB  ILE A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.25e-01
  chirality pdb=" CB  VAL A 199 "
            pdb=" CA  VAL A 199 "
            pdb=" CG1 VAL A 199 "
            pdb=" CG2 VAL A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.02e-01
  chirality pdb=" CG  LEU A1143 "
            pdb=" CB  LEU A1143 "
            pdb=" CD1 LEU A1143 "
            pdb=" CD2 LEU A1143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 2311 not shown)

  Planarity restraints: 2458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 430 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.33e+00
        pdb=" C   LEU A 430 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU A 430 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR A 431 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 431 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.86e+00
        pdb=" C   THR A 431 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 431 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A 432 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 203 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.28e+00
        pdb=" N   PRO A 204 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2455 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 102
        2.56 -     3.15: 11360
        3.15 -     3.73: 21932
        3.73 -     4.32: 34355
        4.32 -     4.90: 53876
  Nonbonded interactions: 121625
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 680 "
            pdb="MG    MG A1302 "
     model   vdw
     1.980 2.170
  nonbonded pdb=" O1A GTP M   2 "
            pdb="MG    MG A1301 "
     model   vdw
     2.056 2.170
  nonbonded pdb=" NE2 GLN A 939 "
            pdb=" O   ILE B  68 "
     model   vdw
     2.206 2.520
  nonbonded pdb=" O   VAL A 548 "
            pdb="MG    MG A1302 "
     model   vdw
     2.207 2.170
  nonbonded pdb=" OG1 THR A 209 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.226 2.440
  ... (remaining 121620 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:             0.020
  Extract box with map and model:          4.450
  Check model and map are aligned:         0.200
  Set scattering table:                    0.130
  Process input model:                     44.000
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:12.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.301  14949  Z= 0.581
  Angle     :  0.721  20.440  20437  Z= 0.397
  Chirality :  0.042   0.192   2314
  Planarity :  0.004   0.038   2458
  Dihedral  : 15.288 170.453   5705
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  6.52 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -4.19 (0.16), residues: 1701
  helix: -3.67 (0.10), residues: 812
  sheet: -1.49 (0.35), residues: 177
  loop : -1.74 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 256 
 HIS   0.006   0.001   HIS B 490 
 PHE   0.018   0.002   PHE A 344 
 TYR   0.014   0.002   TYR B 178 
 ARG   0.011   0.001   ARG A 168 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 261
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 TYR cc_start: 0.8388 (p90) cc_final: 0.7828 (p90)
REVERT: A   92 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: A  484 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7242 (ttp80)
REVERT: A  947 GLU cc_start: 0.7241 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: A 1009 TYR cc_start: 0.8260 (t80) cc_final: 0.7802 (t80)
REVERT: B  132 ILE cc_start: 0.8888 (mm) cc_final: 0.8592 (tt)
REVERT: B  251 ILE cc_start: 0.9004 (pt) cc_final: 0.8636 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 263
  average time/residue: 1.5618
  time to fit residues: 443.6847
Evaluate side-chains
  197 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 195
  time to evaluate  : 1.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  895 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    9.9990
   chunk 130 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 134 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 156 optimal weight:    5.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A 137 GLN
A 378 HIS
A 387 ASN
A 394 GLN
A 412 HIS
A 486 GLN
A 514 ASN
A 617 GLN
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 HIS
A1020 HIS
A1095 GLN
B  53 HIS
B 180 GLN
B 346 ASN
B 542 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14949  Z= 0.205
  Angle     :  0.516   8.697  20437  Z= 0.264
  Chirality :  0.040   0.183   2314
  Planarity :  0.004   0.039   2458
  Dihedral  : 11.732 156.909   2457
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.31 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.19 (0.18), residues: 1701
  helix: -1.51 (0.15), residues: 817
  sheet: -0.96 (0.37), residues: 177
  loop : -1.31 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 260 
 HIS   0.005   0.001   HIS B  59 
 PHE   0.012   0.001   PHE A 206 
 TYR   0.012   0.001   TYR A 563 
 ARG   0.004   0.000   ARG B 518 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 1.708 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8325 (p90) cc_final: 0.7816 (p90)
REVERT: A  317 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8307 (ttt90)
REVERT: A  484 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7286 (ttp80)
REVERT: A  519 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6791 (pp30)
REVERT: A 1009 TYR cc_start: 0.8326 (t80) cc_final: 0.7786 (t80)
REVERT: A 1153 ASP cc_start: 0.8150 (p0) cc_final: 0.7891 (p0)
REVERT: B  251 ILE cc_start: 0.8968 (pt) cc_final: 0.8626 (mt)
REVERT: B  276 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7551 (ttm170)
REVERT: B  281 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7223 (t70)
  outliers start: 33
  outliers final: 13
  residues processed: 237
  average time/residue: 1.3710
  time to fit residues: 353.6657
Evaluate side-chains
  215 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  519 GLN
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  899 GLU
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  480 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 48 optimal weight:    8.9990
   chunk 129 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 156 optimal weight:    8.9990
   chunk 169 optimal weight:    5.9990
   chunk 139 optimal weight:    9.9990
   chunk 155 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 125 optimal weight:    0.0070
   overall best weight:    6.0006

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN
A 387 ASN
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14949  Z= 0.288
  Angle     :  0.542   8.754  20437  Z= 0.273
  Chirality :  0.041   0.170   2314
  Planarity :  0.004   0.037   2458
  Dihedral  : 11.628 158.648   2454
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 14.99 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -1.24 (0.19), residues: 1701
  helix: -0.46 (0.17), residues: 814
  sheet: -0.79 (0.37), residues: 172
  loop : -1.11 (0.22), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 389 
 HIS   0.006   0.001   HIS A1036 
 PHE   0.014   0.001   PHE A 206 
 TYR   0.012   0.001   TYR A 563 
 ARG   0.006   0.001   ARG B 310 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 203
  time to evaluate  : 1.602 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8337 (p90) cc_final: 0.7872 (p90)
REVERT: A   54 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7449 (m-30)
REVERT: A 1009 TYR cc_start: 0.8359 (t80) cc_final: 0.7788 (t80)
REVERT: A 1138 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6604 (tt0)
REVERT: B  251 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8587 (mt)
REVERT: B  276 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7548 (ttm170)
REVERT: B  517 MET cc_start: 0.8804 (mmp) cc_final: 0.8515 (mmp)
  outliers start: 60
  outliers final: 28
  residues processed: 240
  average time/residue: 1.4360
  time to fit residues: 374.9686
Evaluate side-chains
  229 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 198
  time to evaluate  : 1.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 154 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   chunk 157 optimal weight:    0.6980
   chunk 166 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 148 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14949  Z= 0.232
  Angle     :  0.508   8.723  20437  Z= 0.256
  Chirality :  0.040   0.161   2314
  Planarity :  0.004   0.038   2458
  Dihedral  : 11.427 160.619   2454
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.73 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.77 (0.19), residues: 1701
  helix: -0.02 (0.18), residues: 821
  sheet: -0.55 (0.38), residues: 172
  loop : -0.95 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.005   0.001   HIS A1203 
 PHE   0.012   0.001   PHE A 206 
 TYR   0.015   0.001   TYR B 386 
 ARG   0.006   0.000   ARG B 310 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 206
  time to evaluate  : 1.504 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8326 (p90) cc_final: 0.7863 (p90)
REVERT: A   54 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7382 (m-30)
REVERT: A  485 ARG cc_start: 0.7399 (mtp180) cc_final: 0.7087 (mtm-85)
REVERT: A  681 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8281 (t0)
REVERT: A  827 LEU cc_start: 0.8159 (pt) cc_final: 0.7946 (mt)
REVERT: A 1009 TYR cc_start: 0.8403 (t80) cc_final: 0.7809 (t80)
REVERT: A 1138 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6475 (tt0)
REVERT: B  251 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8586 (mt)
REVERT: B  276 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7543 (ttm170)
REVERT: B  281 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7413 (t70)
  outliers start: 60
  outliers final: 37
  residues processed: 243
  average time/residue: 1.3785
  time to fit residues: 365.4517
Evaluate side-chains
  238 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 196
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  130 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  681 ASP
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 ILE
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 138 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 141 optimal weight:   10.0000
   chunk 114 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 149 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14949  Z= 0.261
  Angle     :  0.526  10.237  20437  Z= 0.263
  Chirality :  0.041   0.162   2314
  Planarity :  0.004   0.038   2458
  Dihedral  : 11.367 160.400   2454
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 15.05 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.50 (0.20), residues: 1701
  helix:  0.23 (0.18), residues: 818
  sheet: -0.43 (0.39), residues: 172
  loop : -0.85 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.005   0.001   HIS A1036 
 PHE   0.013   0.001   PHE A 206 
 TYR   0.012   0.001   TYR B 386 
 ARG   0.006   0.000   ARG A 841 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 202
  time to evaluate  : 1.742 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8350 (p90) cc_final: 0.7880 (p90)
REVERT: A   54 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7393 (m-30)
REVERT: A  681 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8266 (t0)
REVERT: A  827 LEU cc_start: 0.8192 (pt) cc_final: 0.7907 (mt)
REVERT: A 1009 TYR cc_start: 0.8345 (t80) cc_final: 0.7825 (t80)
REVERT: A 1138 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6511 (tt0)
REVERT: B  251 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8587 (mt)
REVERT: B  276 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7539 (ttm170)
REVERT: B  281 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7287 (t70)
  outliers start: 75
  outliers final: 42
  residues processed: 248
  average time/residue: 1.3559
  time to fit residues: 367.3924
Evaluate side-chains
  247 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  681 ASP
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1014 MET
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 149 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 166 optimal weight:   20.0000
   chunk 138 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 160 optimal weight:    0.0970
   overall best weight:    5.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 387 ASN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14949  Z= 0.251
  Angle     :  0.524   9.446  20437  Z= 0.261
  Chirality :  0.040   0.162   2314
  Planarity :  0.004   0.039   2458
  Dihedral  : 11.292 159.904   2454
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 15.99 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.40 (0.20), residues: 1701
  helix:  0.31 (0.18), residues: 819
  sheet: -0.33 (0.39), residues: 172
  loop : -0.80 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 260 
 HIS   0.005   0.001   HIS A1036 
 PHE   0.012   0.001   PHE A 206 
 TYR   0.012   0.001   TYR A 563 
 ARG   0.006   0.000   ARG A 841 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 203
  time to evaluate  : 1.619 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8339 (p90) cc_final: 0.7887 (p90)
REVERT: A   54 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7391 (m-30)
REVERT: A  203 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8808 (mp)
REVERT: A  681 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (t0)
REVERT: A  812 MET cc_start: 0.7341 (ptm) cc_final: 0.7098 (ptm)
REVERT: A  827 LEU cc_start: 0.8190 (pt) cc_final: 0.7912 (mt)
REVERT: A  979 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8031 (ttpp)
REVERT: A 1009 TYR cc_start: 0.8378 (t80) cc_final: 0.7808 (t80)
REVERT: A 1138 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6574 (tt0)
REVERT: B  251 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8591 (mt)
REVERT: B  276 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7537 (ttm170)
REVERT: B  281 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7261 (t70)
REVERT: B  359 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8004 (ptpt)
  outliers start: 69
  outliers final: 42
  residues processed: 248
  average time/residue: 1.3906
  time to fit residues: 377.3155
Evaluate side-chains
  246 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 197
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  681 ASP
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 ILE
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 LYS
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 121 optimal weight:    5.9990
   chunk 140 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 165 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 102 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 387 ASN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14949  Z= 0.242
  Angle     :  0.526   8.988  20437  Z= 0.261
  Chirality :  0.040   0.164   2314
  Planarity :  0.004   0.039   2458
  Dihedral  : 11.201 155.963   2454
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 16.53 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.31 (0.20), residues: 1701
  helix:  0.38 (0.18), residues: 820
  sheet: -0.29 (0.39), residues: 172
  loop : -0.75 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.005   0.001   HIS A1036 
 PHE   0.013   0.001   PHE A 902 
 TYR   0.012   0.001   TYR A 563 
 ARG   0.006   0.000   ARG A 841 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 205
  time to evaluate  : 1.673 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8334 (p90) cc_final: 0.7886 (p90)
REVERT: A   54 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7388 (m-30)
REVERT: A  203 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8802 (mp)
REVERT: A  681 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (t0)
REVERT: A  812 MET cc_start: 0.7314 (ptm) cc_final: 0.7043 (ptm)
REVERT: A  827 LEU cc_start: 0.8181 (pt) cc_final: 0.7857 (mt)
REVERT: A  979 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8027 (ttpp)
REVERT: A 1009 TYR cc_start: 0.8384 (t80) cc_final: 0.7823 (t80)
REVERT: A 1138 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6649 (tt0)
REVERT: B  251 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8582 (mt)
REVERT: B  276 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7530 (ttm170)
REVERT: B  281 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7319 (t70)
REVERT: B  359 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7964 (ptpt)
  outliers start: 65
  outliers final: 42
  residues processed: 246
  average time/residue: 1.3805
  time to fit residues: 370.4793
Evaluate side-chains
  248 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 199
  time to evaluate  : 1.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  681 ASP
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 ILE
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 LYS
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 130 optimal weight:   10.0000
   chunk 150 optimal weight:    9.9990
   chunk 158 optimal weight:    9.9990
   chunk 144 optimal weight:    8.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14949  Z= 0.276
  Angle     :  0.543   9.746  20437  Z= 0.270
  Chirality :  0.041   0.172   2314
  Planarity :  0.004   0.039   2458
  Dihedral  : 11.189 147.273   2454
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 16.94 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.34 (0.20), residues: 1701
  helix:  0.32 (0.18), residues: 821
  sheet: -0.27 (0.39), residues: 172
  loop : -0.75 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.005   0.001   HIS A1036 
 PHE   0.015   0.001   PHE A 902 
 TYR   0.012   0.001   TYR A 563 
 ARG   0.006   0.000   ARG A 841 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 201
  time to evaluate  : 1.690 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8342 (p90) cc_final: 0.7882 (p90)
REVERT: A   54 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7395 (m-30)
REVERT: A  203 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8793 (mp)
REVERT: A  485 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6965 (mtm-85)
REVERT: A  681 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (t0)
REVERT: A  812 MET cc_start: 0.7344 (ptm) cc_final: 0.7063 (ptm)
REVERT: A  827 LEU cc_start: 0.8227 (pt) cc_final: 0.7850 (mt)
REVERT: A  979 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8088 (ttpp)
REVERT: A 1009 TYR cc_start: 0.8412 (t80) cc_final: 0.7842 (t80)
REVERT: A 1138 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6649 (tt0)
REVERT: B  251 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8590 (mt)
REVERT: B  276 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7530 (ttm170)
REVERT: B  281 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7361 (t70)
  outliers start: 64
  outliers final: 44
  residues processed: 243
  average time/residue: 1.4139
  time to fit residues: 377.8248
Evaluate side-chains
  244 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 194
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  681 ASP
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 ILE
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 154 optimal weight:    9.9990
   chunk 158 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 139 optimal weight:    5.9990
   chunk 146 optimal weight:    0.8980
   chunk 153 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 163 optimal weight:    0.9980
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 387 ASN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14949  Z= 0.153
  Angle     :  0.488  10.121  20437  Z= 0.242
  Chirality :  0.038   0.163   2314
  Planarity :  0.003   0.040   2458
  Dihedral  : 10.879 136.009   2454
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.15 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.08 (0.20), residues: 1701
  helix:  0.58 (0.18), residues: 820
  sheet: -0.22 (0.39), residues: 170
  loop : -0.65 (0.23), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 260 
 HIS   0.004   0.001   HIS A1203 
 PHE   0.015   0.001   PHE A 902 
 TYR   0.010   0.001   TYR A 563 
 ARG   0.006   0.000   ARG A 841 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 199
  time to evaluate  : 1.646 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8293 (p90) cc_final: 0.7861 (p90)
REVERT: A   54 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7379 (m-30)
REVERT: A  203 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8777 (mp)
REVERT: A  812 MET cc_start: 0.7270 (ptm) cc_final: 0.6939 (ptm)
REVERT: A  830 LEU cc_start: 0.8399 (mp) cc_final: 0.8164 (mp)
REVERT: A 1009 TYR cc_start: 0.8346 (t80) cc_final: 0.7770 (t80)
REVERT: A 1138 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6580 (tt0)
REVERT: B  251 ILE cc_start: 0.8913 (pt) cc_final: 0.8551 (mt)
REVERT: B  276 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7519 (ttm170)
  outliers start: 49
  outliers final: 31
  residues processed: 233
  average time/residue: 1.3765
  time to fit residues: 350.2186
Evaluate side-chains
  223 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  130 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 113 optimal weight:   20.0000
   chunk 171 optimal weight:   50.0000
   chunk 157 optimal weight:    0.9980
   chunk 136 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 105 optimal weight:    3.9990
   chunk 83 optimal weight:   30.0000
   chunk 108 optimal weight:   20.0000
   chunk 145 optimal weight:   20.0000
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 GLN
A 717 GLN
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14949  Z= 0.211
  Angle     :  0.516  10.297  20437  Z= 0.257
  Chirality :  0.040   0.167   2314
  Planarity :  0.004   0.045   2458
  Dihedral  : 10.835 127.720   2454
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.41 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -0.07 (0.20), residues: 1701
  helix:  0.56 (0.18), residues: 820
  sheet: -0.16 (0.39), residues: 172
  loop : -0.61 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.004   0.001   HIS A1036 
 PHE   0.016   0.001   PHE A 902 
 TYR   0.011   0.001   TYR A 563 
 ARG   0.006   0.000   ARG A 484 

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

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

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3402 Ramachandran restraints generated.
    1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 193
  time to evaluate  : 1.308 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.8308 (p90) cc_final: 0.7872 (p90)
REVERT: A   54 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7387 (m-30)
REVERT: A  203 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8776 (mp)
REVERT: A  812 MET cc_start: 0.7281 (ptm) cc_final: 0.6930 (ptm)
REVERT: A 1009 TYR cc_start: 0.8368 (t80) cc_final: 0.7844 (t80)
REVERT: A 1138 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6640 (tt0)
REVERT: B  276 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7522 (ttm170)
  outliers start: 42
  outliers final: 32
  residues processed: 223
  average time/residue: 1.4390
  time to fit residues: 348.8642
Evaluate side-chains
  225 residues out of total 1488 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  471 LYS
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  766 ASP
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  920 VAL
Chi-restraints excluded: chain A residue  987 THR
Chi-restraints excluded: chain A residue 1042 TYR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1115 SER
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1159 GLU
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 CYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  514 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 136 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 140 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 119 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 GLN
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.097401 restraints weight = 17467.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.36
r_work: 0.2883 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14949  Z= 0.152
  Angle     :  0.485  10.294  20437  Z= 0.243
  Chirality :  0.038   0.165   2314
  Planarity :  0.003   0.044   2458
  Dihedral  : 10.610 118.289   2454
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.48 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.07 (0.20), residues: 1701
  helix:  0.70 (0.18), residues: 820
  sheet: -0.20 (0.39), residues: 170
  loop : -0.55 (0.23), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.004   0.001   HIS A1203 
 PHE   0.017   0.001   PHE A 902 
 TYR   0.010   0.001   TYR A 563 
 ARG   0.005   0.000   ARG A 484 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5803.61 seconds
wall clock time: 102 minutes 56.34 seconds (6176.34 seconds total)