Starting phenix.real_space_refine
on Wed Mar  4 04:27:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hvh_35043/03_2026/8hvh_35043.map"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    6963      2.51       5
     N    1794      2.21       5
     O    1891      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1364, 10704
          Classifications: {'peptide': 1364}
          Link IDs: {'PTRANS': 59, 'TRANS': 1304}
          Chain breaks: 2
  Time building chain proxies: 2.55, per 1000 atoms: 0.24
  Number of scatterers: 10704
  At special positions: 0
  Unit cell: (72.76, 113.42, 153.01, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1891      8.00
     N    1794      7.00
     C    6963      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 496.7 milliseconds
  

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2560

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 6 sheets defined
      62.7% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.573A  pdb=" N   TRP A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      Proline residue:  A  41  - end of helix
      removed outlier: 4.139A  pdb=" N   TRP A  46 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL A  47 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.938A  pdb=" N   LEU A  54 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 58
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.605A  pdb=" N   LEU A  72 " --> pdb=" O   HIS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 93
      removed outlier: 4.070A  pdb=" N   VAL A  78 " --> pdb=" O   MET A  74 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   SER A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A  87 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 106
      removed outlier: 3.992A  pdb=" N   PHE A 106 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.935A  pdb=" N   LEU A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLN A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 153
      removed outlier: 3.629A  pdb=" N   ILE A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      Proline residue:  A 151  - end of helix
    Processing helix  chain 'A' and resid 154 through 159
      removed outlier: 5.428A  pdb=" N   LEU A 157 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 174
    Processing helix  chain 'A' and resid 175 through 189
      removed outlier: 3.550A  pdb=" N   LEU A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 181 " --> pdb=" O   HIS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 219
    Processing helix  chain 'A' and resid 223 through 233
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 265
    Processing helix  chain 'A' and resid 299 through 308
    Processing helix  chain 'A' and resid 313 through 323
      removed outlier: 3.814A  pdb=" N   PHE A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 340
      removed outlier: 4.048A  pdb=" N   GLN A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 359
      removed outlier: 4.069A  pdb=" N   GLY A 349 " --> pdb=" O   PRO A 345 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 356 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 375
      removed outlier: 3.636A  pdb=" N   HIS A 372 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 373 " --> pdb=" O   HIS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 394
      removed outlier: 3.817A  pdb=" N   LEU A 394 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 403
    Processing helix  chain 'A' and resid 410 through 415
    Processing helix  chain 'A' and resid 422 through 427
      removed outlier: 4.381A  pdb=" N   PHE A 426 " --> pdb=" O   ASP A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 449
      removed outlier: 3.994A  pdb=" N   ALA A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN A 447 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 462
      removed outlier: 3.921A  pdb=" N   MET A 459 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 467
    Processing helix  chain 'A' and resid 474 through 497
      removed outlier: 3.832A  pdb=" N   LYS A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLN A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   MET A 481 " --> pdb=" O   GLN A 477 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A 484 " --> pdb=" O   GLN A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 504
    Processing helix  chain 'A' and resid 506 through 526
      removed outlier: 3.566A  pdb=" N   ILE A 517 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU A 521 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 541 through 557
      removed outlier: 3.771A  pdb=" N   THR A 547 " --> pdb=" O   PRO A 543 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 556 " --> pdb=" O   TRP A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 583
      removed outlier: 3.642A  pdb=" N   SER A 571 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU A 580 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
    Processing helix  chain 'A' and resid 584 through 595
      removed outlier: 3.668A  pdb=" N   LEU A 588 " --> pdb=" O   MET A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
      removed outlier: 3.504A  pdb=" N   LYS A 600 " --> pdb=" O   SER A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 676
      removed outlier: 3.697A  pdb=" N   VAL A 671 " --> pdb=" O   LYS A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 711
    Processing helix  chain 'A' and resid 716 through 727
      removed outlier: 3.662A  pdb=" N   GLN A 722 " --> pdb=" O   LYS A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 736
      removed outlier: 4.297A  pdb=" N   MET A 735 " --> pdb=" O   ALA A 731 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A 736 " --> pdb=" O   ASP A 732 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 731 through 736'
    Processing helix  chain 'A' and resid 752 through 768
    Processing helix  chain 'A' and resid 782 through 793
    Processing helix  chain 'A' and resid 834 through 841
    Processing helix  chain 'A' and resid 843 through 849
    Processing helix  chain 'A' and resid 955 through 967
      removed outlier: 3.868A  pdb=" N   PHE A 959 " --> pdb=" O   GLU A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 976
    Processing helix  chain 'A' and resid 977 through 996
    Processing helix  chain 'A' and resid 1007 through 1020
      removed outlier: 3.659A  pdb=" N   TYR A1015 " --> pdb=" O   ARG A1011 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU A1018 " --> pdb=" O   VAL A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1053
      removed outlier: 3.878A  pdb=" N   ALA A1032 " --> pdb=" O   LEU A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1063
      removed outlier: 3.692A  pdb=" N   PHE A1060 " --> pdb=" O   PRO A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1072
      removed outlier: 3.538A  pdb=" N   ILE A1068 " --> pdb=" O   PRO A1064 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A1069 " --> pdb=" O   SER A1065 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN A1070 " --> pdb=" O   GLY A1066 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   CYS A1071 " --> pdb=" O   ARG A1067 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A1072 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1064 through 1072'
    Processing helix  chain 'A' and resid 1073 through 1082
      removed outlier: 3.639A  pdb=" N   TYR A1077 " --> pdb=" O   SER A1073 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A1078 " --> pdb=" O   LYS A1074 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   VAL A1079 " --> pdb=" O   ASP A1075 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A1082 " --> pdb=" O   VAL A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1095
    Processing helix  chain 'A' and resid 1098 through 1108
      removed outlier: 3.615A  pdb=" N   ILE A1104 " --> pdb=" O   THR A1100 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   MET A1105 " --> pdb=" O   LEU A1101 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A1106 " --> pdb=" O   VAL A1102 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER A1107 " --> pdb=" O   VAL A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1115
    Processing helix  chain 'A' and resid 1116 through 1153
      removed outlier: 3.775A  pdb=" N   TYR A1122 " --> pdb=" O   LEU A1118 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A1131 " --> pdb=" O   ARG A1127 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   THR A1132 " --> pdb=" O   PHE A1128 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLN A1135 " --> pdb=" O   ALA A1131 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A1137 " --> pdb=" O   SER A1133 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER A1143 " --> pdb=" O   LEU A1139 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   SER A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      Proline residue:  A1146  - end of helix
      removed outlier: 3.982A  pdb=" N   GLU A1153 " --> pdb=" O   SER A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1157 through 1164
    Processing helix  chain 'A' and resid 1166 through 1186
      removed outlier: 3.625A  pdb=" N   PHE A1170 " --> pdb=" O   ARG A1166 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA A1180 " --> pdb=" O   THR A1176 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN A1181 " --> pdb=" O   LYS A1177 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A1184 " --> pdb=" O   ALA A1180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1192 through 1200
      removed outlier: 3.702A  pdb=" N   GLY A1198 " --> pdb=" O   TRP A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1217
      removed outlier: 4.006A  pdb=" N   VAL A1207 " --> pdb=" O   GLY A1203 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A1211 " --> pdb=" O   VAL A1207 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA A1214 " --> pdb=" O   ALA A1210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1224 through 1232
    Processing helix  chain 'A' and resid 1233 through 1236
    Processing helix  chain 'A' and resid 1237 through 1254
      removed outlier: 3.524A  pdb=" N   ASN A1241 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TRP A1242 " --> pdb=" O   PHE A1238 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU A1251 " --> pdb=" O   MET A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1254 through 1264
      removed outlier: 3.711A  pdb=" N   GLU A1258 " --> pdb=" O   ILE A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1328 through 1334
      removed outlier: 3.559A  pdb=" N   THR A1333 " --> pdb=" O   LYS A1329 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A1334 " --> pdb=" O   SER A1330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1353 through 1357
      removed outlier: 3.531A  pdb=" N   ILE A1357 " --> pdb=" O   VAL A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1358 through 1363
    Processing helix  chain 'A' and resid 1391 through 1402
    Processing helix  chain 'A' and resid 1404 through 1411
    Processing helix  chain 'A' and resid 1413 through 1417
    Processing helix  chain 'A' and resid 1427 through 1443
    Processing helix  chain 'A' and resid 1457 through 1472
    Processing helix  chain 'A' and resid 1483 through 1488
      removed outlier: 4.037A  pdb=" N   ILE A1487 " --> pdb=" O   ARG A1483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1513
    Processing helix  chain 'A' and resid 1515 through 1523
    Processing sheet with id=AA1, first strand: chain 'A' and resid 616 through 617
      removed outlier: 4.336A  pdb=" N   ALA A 626 " --> pdb=" O   PRO A 652 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   THR A 628 " --> pdb=" O   GLN A 650 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   GLN A 650 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   HIS A 630 " --> pdb=" O   ASP A 648 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ASP A 648 " --> pdb=" O   HIS A 630 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   GLY A 632 " --> pdb=" O   SER A 646 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617
      removed outlier: 3.740A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   THR A 635 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LYS A 680 " --> pdb=" O   THR A 635 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 691 through 694
      removed outlier: 6.255A  pdb=" N   PHE A 772 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL A 808 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A 774 " --> pdb=" O   VAL A 808 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 657 " --> pdb=" O   ARG A 805 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   LEU A 656 " --> pdb=" O   PHE A 820 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   ILE A 822 " --> pdb=" O   LEU A 656 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ALA A 658 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   LEU A 824 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A 660 " --> pdb=" O   LEU A 824 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE A 821 " --> pdb=" O   MET A 832 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET A 832 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL A 823 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 703 through 704
      removed outlier: 3.631A  pdb=" N   CYS A 703 " --> pdb=" O   ILE A 744 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1306 through 1313
      removed outlier: 6.063A  pdb=" N   ARG A1307 " --> pdb=" O   VAL A1296 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   VAL A1296 " --> pdb=" O   ARG A1307 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   LEU A1311 " --> pdb=" O   ARG A1292 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ARG A1292 " --> pdb=" O   LEU A1311 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A1313 " --> pdb=" O   GLU A1290 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   GLU A1290 " --> pdb=" O   VAL A1313 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TYR A1294 " --> pdb=" O   LYS A1344 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LYS A1344 " --> pdb=" O   TYR A1294 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1366 through 1369
      removed outlier: 6.802A  pdb=" N   THR A1367 " --> pdb=" O   VAL A1448 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ASP A1450 " --> pdb=" O   THR A1367 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ILE A1369 " --> pdb=" O   ASP A1450 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   LEU A1447 " --> pdb=" O   LEU A1478 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   ILE A1480 " --> pdb=" O   LEU A1447 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A1449 " --> pdb=" O   ILE A1480 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   LYS A1318 " --> pdb=" O   ARG A1492 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU A1494 " --> pdb=" O   LYS A1318 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   GLY A1320 " --> pdb=" O   LEU A1494 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU A1496 " --> pdb=" O   GLY A1320 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL A1322 " --> pdb=" O   LEU A1496 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A1503 " --> pdb=" O   VAL A1495 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ASP A1497 " --> pdb=" O   VAL A1501 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   VAL A1501 " --> pdb=" O   ASP A1497 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3295
        1.34 -     1.45: 1733
        1.45 -     1.57: 5835
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 10953
  Sorted by residual:
  bond pdb=" CA  SER A 216 "
       pdb=" C   SER A 216 "
    ideal  model  delta    sigma   weight residual
    1.524  1.464  0.059 2.25e-02 1.98e+03 6.92e+00
  bond pdb=" CG  LEU A 243 "
       pdb=" CD2 LEU A 243 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.45e+00
  bond pdb=" CG1 ILE A1190 "
       pdb=" CD1 ILE A1190 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 1.96e+00
  bond pdb=" C   SER A 216 "
       pdb=" O   SER A 216 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.021 1.62e-02 3.81e+03 1.64e+00
  bond pdb=" CG  LEU A1250 "
       pdb=" CD1 LEU A1250 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  ... (remaining 10948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 14437
        1.91 -     3.83: 387
        3.83 -     5.74: 53
        5.74 -     7.66: 15
        7.66 -     9.57: 4
  Bond angle restraints: 14896
  Sorted by residual:
  angle pdb=" N   ILE A 498 "
        pdb=" CA  ILE A 498 "
        pdb=" C   ILE A 498 "
      ideal   model   delta    sigma   weight residual
     112.96  108.11    4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" N   VAL A 111 "
        pdb=" CA  VAL A 111 "
        pdb=" C   VAL A 111 "
      ideal   model   delta    sigma   weight residual
     113.53  109.08    4.45 9.80e-01 1.04e+00 2.07e+01
  angle pdb=" C   ILE A 385 "
        pdb=" N   MET A 386 "
        pdb=" CA  MET A 386 "
      ideal   model   delta    sigma   weight residual
     122.31  115.30    7.01 2.00e+00 2.50e-01 1.23e+01
  angle pdb=" N   VAL A1014 "
        pdb=" CA  VAL A1014 "
        pdb=" C   VAL A1014 "
      ideal   model   delta    sigma   weight residual
     112.98  108.91    4.07 1.25e+00 6.40e-01 1.06e+01
  angle pdb=" N   PRO A 103 "
        pdb=" CD  PRO A 103 "
        pdb=" CG  PRO A 103 "
      ideal   model   delta    sigma   weight residual
     103.20   98.48    4.72 1.50e+00 4.44e-01 9.91e+00
  ... (remaining 14891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 5833
       17.85 -    35.70: 554
       35.70 -    53.55: 81
       53.55 -    71.40: 20
       71.40 -    89.25: 8
  Dihedral angle restraints: 6496
    sinusoidal: 2534
      harmonic: 3962
  Sorted by residual:
  dihedral pdb=" CA  TYR A1186 "
           pdb=" C   TYR A1186 "
           pdb=" N   PRO A1187 "
           pdb=" CA  PRO A1187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.86   26.14     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  GLN A 436 "
           pdb=" C   GLN A 436 "
           pdb=" N   ILE A 437 "
           pdb=" CA  ILE A 437 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  GLU A 209 "
           pdb=" C   GLU A 209 "
           pdb=" N   THR A 210 "
           pdb=" CA  THR A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.53   20.47     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 6493 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1119
       0.041 -    0.082: 479
       0.082 -    0.123: 119
       0.123 -    0.164: 18
       0.164 -    0.204: 2
  Chirality restraints: 1737
  Sorted by residual:
  chirality pdb=" CG  LEU A 137 "
            pdb=" CB  LEU A 137 "
            pdb=" CD1 LEU A 137 "
            pdb=" CD2 LEU A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  PHE A 196 "
            pdb=" N   PHE A 196 "
            pdb=" C   PHE A 196 "
            pdb=" CB  PHE A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CA  ASN A1165 "
            pdb=" N   ASN A1165 "
            pdb=" C   ASN A1165 "
            pdb=" CB  ASN A1165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.37e-01
  ... (remaining 1734 not shown)

  Planarity restraints: 1862
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 328 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO A 329 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1116 "   -0.033 5.00e-02 4.00e+02   5.04e-02 4.06e+00
        pdb=" N   PRO A1117 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A1117 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1117 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 542 "   -0.030 5.00e-02 4.00e+02   4.45e-02 3.16e+00
        pdb=" N   PRO A 543 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1859 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 167
        2.67 -     3.22: 10778
        3.22 -     3.78: 16458
        3.78 -     4.34: 23189
        4.34 -     4.90: 37230
  Nonbonded interactions: 87822
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" O   SER A 216 "
            pdb=" OG  SER A 216 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ALA A 764 "
            pdb=" OG  SER A 767 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ASP A1461 "
            pdb=" NE2 GLN A1465 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   THR A1108 "
            pdb=" OG1 THR A1108 "
     model   vdw
     2.279 3.040
  ... (remaining 87817 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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.650
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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      :  0.005   0.059  10953  Z= 0.232
  Angle     :  0.761   9.572  14896  Z= 0.416
  Chirality :  0.046   0.204   1737
  Planarity :  0.005   0.066   1862
  Dihedral  : 14.435  89.249   3936
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.21), residues: 1358
  helix: -2.01 (0.17), residues: 841
  sheet: -0.22 (0.63), residues: 74
  loop : -1.97 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 170 
 TYR   0.018   0.002   TYR A 504 
 PHE   0.029   0.002   PHE A 311 
 TRP   0.015   0.002   TRP A 347 
 HIS   0.006   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (10953)
  covalent geometry    : angle       0.76081 (14896)
  hydrogen bonds       : bond        0.20583 (  488)
  hydrogen bonds       : angle       8.02541 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  404 SER cc_start: 0.7858 (t) cc_final: 0.7404 (m)
REVERT: A  821 ILE cc_start: 0.6691 (mt) cc_final: 0.6355 (mt)
REVERT: A 1115 ILE cc_start: 0.8788 (tp) cc_final: 0.8575 (tp)
REVERT: A 1122 TYR cc_start: 0.7441 (t80) cc_final: 0.7032 (t80)
REVERT: A 1294 TYR cc_start: 0.8157 (t80) cc_final: 0.7907 (t80)
REVERT: A 1321 ILE cc_start: 0.8582 (mm) cc_final: 0.8369 (mm)
REVERT: A 1344 LYS cc_start: 0.7062 (mmtt) cc_final: 0.6636 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1020
  time to fit residues: 40.7366
Evaluate side-chains
  156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN
A 702 ASN
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1046 GLN
A1057 GLN
A1092 ASN
A1181 ASN
A1182 GLN
A1465 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.152926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.109333 restraints weight = 15724.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.43
r_work: 0.3380 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10953  Z= 0.177
  Angle     :  0.727   9.626  14896  Z= 0.367
  Chirality :  0.045   0.170   1737
  Planarity :  0.005   0.061   1862
  Dihedral  :  5.612  23.119   1468
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.56 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.22), residues: 1358
  helix: -1.31 (0.17), residues: 868
  sheet: -0.03 (0.60), residues: 74
  loop : -1.82 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1004 
 TYR   0.018   0.002   TYR A 720 
 PHE   0.025   0.002   PHE A 196 
 TRP   0.015   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (10953)
  covalent geometry    : angle       0.72702 (14896)
  hydrogen bonds       : bond        0.04275 (  488)
  hydrogen bonds       : angle       5.17512 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.8415 (tt) cc_final: 0.8206 (tt)
REVERT: A  244 LYS cc_start: 0.8638 (pttt) cc_final: 0.8243 (pttp)
REVERT: A  251 MET cc_start: 0.9036 (mmm) cc_final: 0.8776 (mmp)
REVERT: A  415 VAL cc_start: 0.8638 (t) cc_final: 0.8294 (m)
REVERT: A  481 MET cc_start: 0.8105 (tpp) cc_final: 0.7785 (tpp)
REVERT: A  715 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (tp)
REVERT: A  766 TYR cc_start: 0.8611 (t80) cc_final: 0.8408 (t80)
REVERT: A  768 ASP cc_start: 0.8851 (m-30) cc_final: 0.8494 (m-30)
REVERT: A  775 ASP cc_start: 0.7934 (m-30) cc_final: 0.7649 (m-30)
REVERT: A  821 ILE cc_start: 0.7151 (mt) cc_final: 0.6931 (mt)
REVERT: A  839 LEU cc_start: 0.6986 (tp) cc_final: 0.6753 (mt)
REVERT: A 1024 PHE cc_start: 0.7372 (m-10) cc_final: 0.6761 (t80)
REVERT: A 1121 LEU cc_start: 0.8693 (tt) cc_final: 0.8484 (tt)
REVERT: A 1122 TYR cc_start: 0.8281 (t80) cc_final: 0.7640 (t80)
REVERT: A 1338 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8532 (mmm-85)
REVERT: A 1344 LYS cc_start: 0.6922 (mmtt) cc_final: 0.6565 (mmmt)
REVERT: A 1353 ASN cc_start: 0.7586 (t0) cc_final: 0.7320 (t0)
REVERT: A 1432 GLN cc_start: 0.8278 (mp10) cc_final: 0.7594 (mp10)
REVERT: A 1488 MET cc_start: 0.8191 (mmm) cc_final: 0.7772 (tmm)
  outliers start: 25
  outliers final: 19
  residues processed: 210
  average time/residue: 0.0904
  time to fit residues: 28.6159
Evaluate side-chains
  176 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  473 MET
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1149 SER
Chi-restraints excluded: chain A residue 1228 LEU
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1296 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 129 optimal weight:    0.6980
   chunk 117 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 519 GLN
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1006 ASN
A1181 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.153982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.109305 restraints weight = 15724.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.49
r_work: 0.3365 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10953  Z= 0.130
  Angle     :  0.626   8.771  14896  Z= 0.313
  Chirality :  0.042   0.158   1737
  Planarity :  0.004   0.041   1862
  Dihedral  :  5.132  24.041   1468
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.92 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.22), residues: 1358
  helix: -0.81 (0.18), residues: 862
  sheet: -0.54 (0.60), residues: 68
  loop : -1.50 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.017   0.001   TYR A 720 
 PHE   0.024   0.001   PHE A 196 
 TRP   0.009   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10953)
  covalent geometry    : angle       0.62584 (14896)
  hydrogen bonds       : bond        0.03676 (  488)
  hydrogen bonds       : angle       4.66191 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.7342 (tt) cc_final: 0.6840 (tp)
REVERT: A  180 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7344 (mp)
REVERT: A  247 ASP cc_start: 0.7971 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  251 MET cc_start: 0.9074 (mmm) cc_final: 0.8805 (mmp)
REVERT: A  415 VAL cc_start: 0.8620 (t) cc_final: 0.8302 (m)
REVERT: A  630 HIS cc_start: 0.6828 (m170) cc_final: 0.6396 (m-70)
REVERT: A  724 LEU cc_start: 0.8384 (mt) cc_final: 0.8106 (mt)
REVERT: A  766 TYR cc_start: 0.8624 (t80) cc_final: 0.8408 (t80)
REVERT: A  768 ASP cc_start: 0.8880 (m-30) cc_final: 0.8508 (m-30)
REVERT: A  775 ASP cc_start: 0.7944 (m-30) cc_final: 0.7650 (m-30)
REVERT: A  832 MET cc_start: 0.6745 (ttt) cc_final: 0.6486 (ttt)
REVERT: A 1024 PHE cc_start: 0.7448 (m-10) cc_final: 0.6962 (t80)
REVERT: A 1063 THR cc_start: 0.8191 (m) cc_final: 0.7717 (p)
REVERT: A 1122 TYR cc_start: 0.8333 (t80) cc_final: 0.7757 (t80)
REVERT: A 1338 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8359 (mmm-85)
REVERT: A 1353 ASN cc_start: 0.7795 (t0) cc_final: 0.7566 (t0)
REVERT: A 1488 MET cc_start: 0.8397 (mmm) cc_final: 0.7777 (tmm)
REVERT: A 1505 ASP cc_start: 0.7563 (t70) cc_final: 0.7217 (t70)
  outliers start: 28
  outliers final: 17
  residues processed: 193
  average time/residue: 0.0831
  time to fit residues: 24.3763
Evaluate side-chains
  173 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  782 ASP
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1149 SER
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1296 VAL
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 133 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 69 optimal weight:    6.9990
   chunk 114 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 55 optimal weight:    0.1980
   chunk 116 optimal weight:    8.9990
   chunk 125 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1465 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.155012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.109776 restraints weight = 15888.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.51
r_work: 0.3378 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10953  Z= 0.114
  Angle     :  0.612   9.771  14896  Z= 0.300
  Chirality :  0.042   0.154   1737
  Planarity :  0.004   0.034   1862
  Dihedral  :  4.824  23.542   1468
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.64 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.23), residues: 1358
  helix: -0.50 (0.18), residues: 854
  sheet: -0.41 (0.61), residues: 68
  loop : -1.36 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.010   0.001   TYR A 720 
 PHE   0.024   0.001   PHE A 196 
 TRP   0.007   0.001   TRP A 347 
 HIS   0.002   0.001   HIS A1360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10953)
  covalent geometry    : angle       0.61159 (14896)
  hydrogen bonds       : bond        0.03217 (  488)
  hydrogen bonds       : angle       4.39708 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.6515 (ttp80) cc_final: 0.6099 (ptm-80)
REVERT: A  180 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7212 (mp)
REVERT: A  251 MET cc_start: 0.9064 (mmm) cc_final: 0.8803 (mmp)
REVERT: A  405 THR cc_start: 0.8683 (m) cc_final: 0.8440 (p)
REVERT: A  415 VAL cc_start: 0.8597 (t) cc_final: 0.8328 (m)
REVERT: A  472 LYS cc_start: 0.8448 (tppt) cc_final: 0.8155 (tttp)
REVERT: A  630 HIS cc_start: 0.6906 (m170) cc_final: 0.6469 (m-70)
REVERT: A  766 TYR cc_start: 0.8572 (t80) cc_final: 0.8366 (t80)
REVERT: A  768 ASP cc_start: 0.8906 (m-30) cc_final: 0.8600 (m-30)
REVERT: A 1024 PHE cc_start: 0.7516 (m-10) cc_final: 0.6990 (t80)
REVERT: A 1063 THR cc_start: 0.8148 (m) cc_final: 0.7690 (p)
REVERT: A 1122 TYR cc_start: 0.8468 (t80) cc_final: 0.8201 (t80)
REVERT: A 1247 MET cc_start: 0.8268 (ttm) cc_final: 0.7941 (ttm)
REVERT: A 1295 SER cc_start: 0.7454 (t) cc_final: 0.7038 (p)
REVERT: A 1338 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8312 (mmm-85)
REVERT: A 1353 ASN cc_start: 0.7949 (t0) cc_final: 0.7665 (t0)
REVERT: A 1488 MET cc_start: 0.8440 (mmm) cc_final: 0.7870 (tmm)
REVERT: A 1505 ASP cc_start: 0.7427 (t70) cc_final: 0.7067 (t70)
  outliers start: 34
  outliers final: 26
  residues processed: 190
  average time/residue: 0.0801
  time to fit residues: 23.2262
Evaluate side-chains
  183 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1296 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1367 THR
Chi-restraints excluded: chain A residue 1432 GLN
Chi-restraints excluded: chain A residue 1501 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:    0.4980
   chunk 91 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 120 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.153477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.108534 restraints weight = 15656.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.50
r_work: 0.3352 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10953  Z= 0.138
  Angle     :  0.622  10.217  14896  Z= 0.302
  Chirality :  0.042   0.137   1737
  Planarity :  0.004   0.033   1862
  Dihedral  :  4.749  24.186   1468
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.15 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.23), residues: 1358
  helix: -0.33 (0.18), residues: 858
  sheet: -0.15 (0.58), residues: 76
  loop : -1.27 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 720 
 PHE   0.022   0.001   PHE A 196 
 TRP   0.007   0.001   TRP A 991 
 HIS   0.006   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10953)
  covalent geometry    : angle       0.62208 (14896)
  hydrogen bonds       : bond        0.03344 (  488)
  hydrogen bonds       : angle       4.31254 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.6445 (ttp80) cc_final: 0.6039 (ptm-80)
REVERT: A  180 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7190 (mp)
REVERT: A  405 THR cc_start: 0.8606 (m) cc_final: 0.8366 (p)
REVERT: A  415 VAL cc_start: 0.8573 (t) cc_final: 0.8310 (m)
REVERT: A  515 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7759 (mm-30)
REVERT: A  630 HIS cc_start: 0.6753 (m170) cc_final: 0.6362 (m-70)
REVERT: A  678 MET cc_start: 0.8222 (mtp) cc_final: 0.7616 (mtp)
REVERT: A  687 MET cc_start: 0.7411 (ttp) cc_final: 0.7083 (ptm)
REVERT: A  724 LEU cc_start: 0.8112 (mt) cc_final: 0.7753 (mt)
REVERT: A  766 TYR cc_start: 0.8649 (t80) cc_final: 0.8253 (t80)
REVERT: A 1024 PHE cc_start: 0.7481 (m-10) cc_final: 0.6966 (t80)
REVERT: A 1063 THR cc_start: 0.8240 (m) cc_final: 0.7831 (p)
REVERT: A 1338 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8397 (mmm-85)
REVERT: A 1488 MET cc_start: 0.8326 (mmm) cc_final: 0.7871 (tmm)
REVERT: A 1505 ASP cc_start: 0.7577 (t70) cc_final: 0.7239 (t0)
  outliers start: 41
  outliers final: 37
  residues processed: 197
  average time/residue: 0.0770
  time to fit residues: 23.5623
Evaluate side-chains
  194 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  953 THR
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1250 LEU
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1275 GLU
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1296 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1367 THR
Chi-restraints excluded: chain A residue 1432 GLN
Chi-restraints excluded: chain A residue 1500 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 32 optimal weight:    0.2980
   chunk 96 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 126 optimal weight:    0.1980
   chunk 90 optimal weight:    0.8980
   chunk 131 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0970
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.2496

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

Flipped N/Q/H residues before XYZ refinement:
A 721 GLN
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.157159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.112041 restraints weight = 15614.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.52
r_work: 0.3402 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10953  Z= 0.101
  Angle     :  0.588   8.684  14896  Z= 0.285
  Chirality :  0.041   0.136   1737
  Planarity :  0.003   0.032   1862
  Dihedral  :  4.517  22.588   1468
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.86 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.23), residues: 1358
  helix: -0.02 (0.18), residues: 854
  sheet: -0.07 (0.60), residues: 76
  loop : -1.11 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1442 
 TYR   0.009   0.001   TYR A1518 
 PHE   0.021   0.001   PHE A 196 
 TRP   0.009   0.001   TRP A 347 
 HIS   0.008   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (10953)
  covalent geometry    : angle       0.58762 (14896)
  hydrogen bonds       : bond        0.02969 (  488)
  hydrogen bonds       : angle       4.14756 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.6412 (ttp80) cc_final: 0.6035 (ptm-80)
REVERT: A  180 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7266 (mp)
REVERT: A  415 VAL cc_start: 0.8607 (t) cc_final: 0.8357 (m)
REVERT: A  515 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7797 (mm-30)
REVERT: A  630 HIS cc_start: 0.6851 (m170) cc_final: 0.6511 (m-70)
REVERT: A  678 MET cc_start: 0.8204 (mtp) cc_final: 0.7671 (mtp)
REVERT: A  687 MET cc_start: 0.7201 (ttp) cc_final: 0.6903 (ptm)
REVERT: A  724 LEU cc_start: 0.8090 (mt) cc_final: 0.7624 (mt)
REVERT: A 1024 PHE cc_start: 0.7367 (m-10) cc_final: 0.6927 (t80)
REVERT: A 1063 THR cc_start: 0.8235 (m) cc_final: 0.7816 (p)
REVERT: A 1338 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8334 (mmm-85)
REVERT: A 1357 ILE cc_start: 0.7400 (mp) cc_final: 0.7191 (mm)
REVERT: A 1488 MET cc_start: 0.8433 (mmm) cc_final: 0.7864 (tmm)
REVERT: A 1505 ASP cc_start: 0.7702 (t70) cc_final: 0.7375 (t0)
  outliers start: 30
  outliers final: 23
  residues processed: 194
  average time/residue: 0.0783
  time to fit residues: 23.3196
Evaluate side-chains
  185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1149 SER
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1432 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0670
   chunk 101 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 115 optimal weight:    9.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 436 GLN
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1253 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.156494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.109822 restraints weight = 15649.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.58
r_work: 0.3374 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10953  Z= 0.110
  Angle     :  0.583   8.728  14896  Z= 0.282
  Chirality :  0.041   0.177   1737
  Planarity :  0.003   0.031   1862
  Dihedral  :  4.435  22.908   1468
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.35 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.23), residues: 1358
  helix:  0.11 (0.18), residues: 854
  sheet: -0.13 (0.59), residues: 76
  loop : -1.01 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 170 
 TYR   0.009   0.001   TYR A1518 
 PHE   0.019   0.001   PHE A 196 
 TRP   0.008   0.001   TRP A 991 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10953)
  covalent geometry    : angle       0.58260 (14896)
  hydrogen bonds       : bond        0.03019 (  488)
  hydrogen bonds       : angle       4.09423 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.6336 (ttp80) cc_final: 0.5980 (ptm-80)
REVERT: A  180 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7171 (mp)
REVERT: A  415 VAL cc_start: 0.8590 (t) cc_final: 0.8369 (m)
REVERT: A  515 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7715 (mm-30)
REVERT: A  630 HIS cc_start: 0.6819 (m170) cc_final: 0.6493 (m-70)
REVERT: A  675 LEU cc_start: 0.9034 (mt) cc_final: 0.8818 (mt)
REVERT: A  678 MET cc_start: 0.7963 (mtp) cc_final: 0.7410 (mtp)
REVERT: A  724 LEU cc_start: 0.8089 (mt) cc_final: 0.7619 (mt)
REVERT: A 1024 PHE cc_start: 0.7209 (m-10) cc_final: 0.6946 (t80)
REVERT: A 1063 THR cc_start: 0.8239 (m) cc_final: 0.7810 (p)
REVERT: A 1247 MET cc_start: 0.8136 (mtp) cc_final: 0.7300 (tpt)
REVERT: A 1338 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8254 (mmm-85)
REVERT: A 1488 MET cc_start: 0.8437 (mmm) cc_final: 0.7831 (tmm)
REVERT: A 1505 ASP cc_start: 0.7697 (t70) cc_final: 0.7410 (t0)
  outliers start: 38
  outliers final: 31
  residues processed: 192
  average time/residue: 0.0796
  time to fit residues: 23.6920
Evaluate side-chains
  185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1149 SER
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1275 GLU
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1432 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 108 optimal weight:    0.6980
   chunk 121 optimal weight:    6.9990
   chunk 107 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 129 optimal weight:    8.9990
   chunk 49 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 436 GLN
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.156625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.109932 restraints weight = 15554.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.53
r_work: 0.3390 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10953  Z= 0.111
  Angle     :  0.586   9.282  14896  Z= 0.285
  Chirality :  0.042   0.182   1737
  Planarity :  0.003   0.032   1862
  Dihedral  :  4.413  22.862   1468
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.12 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.23), residues: 1358
  helix:  0.22 (0.19), residues: 847
  sheet: -0.13 (0.59), residues: 76
  loop : -0.87 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 261 
 TYR   0.008   0.001   TYR A1518 
 PHE   0.018   0.001   PHE A 196 
 TRP   0.011   0.001   TRP A 348 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10953)
  covalent geometry    : angle       0.58599 (14896)
  hydrogen bonds       : bond        0.03036 (  488)
  hydrogen bonds       : angle       4.07340 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8374 (tp) cc_final: 0.8166 (tt)
REVERT: A   99 ARG cc_start: 0.6400 (ttp80) cc_final: 0.5973 (ptm-80)
REVERT: A  415 VAL cc_start: 0.8588 (t) cc_final: 0.8376 (m)
REVERT: A  515 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7903 (mm-30)
REVERT: A  540 MET cc_start: 0.8872 (mmm) cc_final: 0.8641 (mmt)
REVERT: A  630 HIS cc_start: 0.6852 (m170) cc_final: 0.6539 (m-70)
REVERT: A  675 LEU cc_start: 0.9135 (mt) cc_final: 0.8923 (mt)
REVERT: A  678 MET cc_start: 0.8183 (mtp) cc_final: 0.7652 (mtp)
REVERT: A  687 MET cc_start: 0.7255 (ttp) cc_final: 0.6978 (ptm)
REVERT: A  724 LEU cc_start: 0.8223 (mt) cc_final: 0.7852 (mt)
REVERT: A 1024 PHE cc_start: 0.7350 (m-10) cc_final: 0.7055 (t80)
REVERT: A 1063 THR cc_start: 0.8250 (m) cc_final: 0.7827 (p)
REVERT: A 1247 MET cc_start: 0.8326 (mtp) cc_final: 0.7496 (tpt)
REVERT: A 1275 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6736 (mm-30)
REVERT: A 1338 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8416 (mmm-85)
REVERT: A 1436 LEU cc_start: 0.8660 (tt) cc_final: 0.8243 (mt)
REVERT: A 1488 MET cc_start: 0.8441 (mmm) cc_final: 0.7805 (tmm)
REVERT: A 1505 ASP cc_start: 0.7778 (t70) cc_final: 0.7483 (t0)
  outliers start: 35
  outliers final: 29
  residues processed: 187
  average time/residue: 0.0787
  time to fit residues: 22.8616
Evaluate side-chains
  188 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1149 SER
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1275 GLU
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1432 GLN
Chi-restraints excluded: chain A residue 1501 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 128 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0970
   chunk 115 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0870
   chunk 71 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0170
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 GLN
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.158638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.111687 restraints weight = 15532.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.59
r_work: 0.3399 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10953  Z= 0.099
  Angle     :  0.580   9.489  14896  Z= 0.279
  Chirality :  0.041   0.150   1737
  Planarity :  0.003   0.032   1862
  Dihedral  :  4.284  22.424   1468
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.80 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.23), residues: 1358
  helix:  0.33 (0.19), residues: 848
  sheet: -0.14 (0.59), residues: 76
  loop : -0.80 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 261 
 TYR   0.008   0.001   TYR A1518 
 PHE   0.017   0.001   PHE A 196 
 TRP   0.010   0.001   TRP A 347 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10953)
  covalent geometry    : angle       0.57982 (14896)
  hydrogen bonds       : bond        0.02840 (  488)
  hydrogen bonds       : angle       4.01345 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8328 (tp) cc_final: 0.8119 (tt)
REVERT: A   52 TYR cc_start: 0.8668 (t80) cc_final: 0.8397 (t80)
REVERT: A   99 ARG cc_start: 0.6347 (ttp80) cc_final: 0.5938 (ptm-80)
REVERT: A  415 VAL cc_start: 0.8623 (t) cc_final: 0.8386 (m)
REVERT: A  515 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7886 (mm-30)
REVERT: A  630 HIS cc_start: 0.6824 (m170) cc_final: 0.6515 (m-70)
REVERT: A  672 SER cc_start: 0.8231 (m) cc_final: 0.7743 (t)
REVERT: A  678 MET cc_start: 0.8127 (mtp) cc_final: 0.7738 (mtp)
REVERT: A  687 MET cc_start: 0.7210 (ttp) cc_final: 0.6964 (ptm)
REVERT: A  724 LEU cc_start: 0.8166 (mt) cc_final: 0.7803 (mt)
REVERT: A  775 ASP cc_start: 0.8095 (m-30) cc_final: 0.7823 (m-30)
REVERT: A  814 PHE cc_start: 0.8175 (m-80) cc_final: 0.7895 (m-10)
REVERT: A 1024 PHE cc_start: 0.7341 (m-10) cc_final: 0.7011 (t80)
REVERT: A 1063 THR cc_start: 0.8252 (m) cc_final: 0.7820 (p)
REVERT: A 1247 MET cc_start: 0.8391 (mtp) cc_final: 0.7585 (tpt)
REVERT: A 1436 LEU cc_start: 0.8668 (tt) cc_final: 0.8277 (mt)
REVERT: A 1488 MET cc_start: 0.8448 (mmm) cc_final: 0.7779 (tmm)
REVERT: A 1505 ASP cc_start: 0.7800 (t70) cc_final: 0.7472 (t0)
  outliers start: 27
  outliers final: 24
  residues processed: 185
  average time/residue: 0.0748
  time to fit residues: 21.8912
Evaluate side-chains
  187 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1432 GLN
Chi-restraints excluded: chain A residue 1501 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0770
   chunk 66 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    0.2980
   chunk 88 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0170
   chunk 132 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.158882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.111894 restraints weight = 15490.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.59
r_work: 0.3400 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10953  Z= 0.100
  Angle     :  0.579   9.895  14896  Z= 0.277
  Chirality :  0.041   0.155   1737
  Planarity :  0.003   0.032   1862
  Dihedral  :  4.204  22.145   1468
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.89 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.23), residues: 1358
  helix:  0.43 (0.19), residues: 848
  sheet: -0.01 (0.60), residues: 75
  loop : -0.72 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 261 
 TYR   0.008   0.001   TYR A1518 
 PHE   0.017   0.001   PHE A 196 
 TRP   0.009   0.001   TRP A 348 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10953)
  covalent geometry    : angle       0.57888 (14896)
  hydrogen bonds       : bond        0.02784 (  488)
  hydrogen bonds       : angle       3.97432 ( 1416)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 TYR cc_start: 0.8638 (t80) cc_final: 0.8379 (t80)
REVERT: A   99 ARG cc_start: 0.6278 (ttp80) cc_final: 0.5899 (ptm-80)
REVERT: A  415 VAL cc_start: 0.8671 (t) cc_final: 0.8453 (m)
REVERT: A  515 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7757 (mm-30)
REVERT: A  540 MET cc_start: 0.8703 (mmm) cc_final: 0.8473 (mmt)
REVERT: A  630 HIS cc_start: 0.6733 (m170) cc_final: 0.6440 (m-70)
REVERT: A  672 SER cc_start: 0.8105 (m) cc_final: 0.7611 (t)
REVERT: A  678 MET cc_start: 0.7930 (mtp) cc_final: 0.7558 (mtp)
REVERT: A  687 MET cc_start: 0.7064 (ttp) cc_final: 0.6823 (ptm)
REVERT: A  724 LEU cc_start: 0.8167 (mt) cc_final: 0.7788 (mt)
REVERT: A  775 ASP cc_start: 0.8026 (m-30) cc_final: 0.7749 (m-30)
REVERT: A 1063 THR cc_start: 0.8308 (m) cc_final: 0.7888 (p)
REVERT: A 1247 MET cc_start: 0.8084 (mtp) cc_final: 0.7293 (tpt)
REVERT: A 1258 GLU cc_start: 0.8070 (pp20) cc_final: 0.7806 (pp20)
REVERT: A 1436 LEU cc_start: 0.8636 (tt) cc_final: 0.8246 (mt)
REVERT: A 1488 MET cc_start: 0.8386 (mmm) cc_final: 0.7742 (tmm)
REVERT: A 1505 ASP cc_start: 0.7736 (t70) cc_final: 0.7441 (t0)
  outliers start: 25
  outliers final: 24
  residues processed: 183
  average time/residue: 0.0778
  time to fit residues: 22.5716
Evaluate side-chains
  185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  645 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  799 VAL
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1142 VAL
Chi-restraints excluded: chain A residue 1268 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1354 VAL
Chi-restraints excluded: chain A residue 1432 GLN
Chi-restraints excluded: chain A residue 1501 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 68 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.153553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.112683 restraints weight = 15797.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.81
r_work: 0.3306 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10953  Z= 0.173
  Angle     :  0.636   9.755  14896  Z= 0.309
  Chirality :  0.045   0.164   1737
  Planarity :  0.004   0.031   1862
  Dihedral  :  4.489  22.963   1468
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.63 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.23), residues: 1358
  helix:  0.13 (0.18), residues: 853
  sheet: -0.12 (0.60), residues: 75
  loop : -0.78 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1193 
 TYR   0.020   0.002   TYR A  44 
 PHE   0.017   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A 995 
 HIS   0.006   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10953)
  covalent geometry    : angle       0.63598 (14896)
  hydrogen bonds       : bond        0.03495 (  488)
  hydrogen bonds       : angle       4.18072 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3059.06 seconds
wall clock time: 52 minutes 51.15 seconds (3171.15 seconds total)