Starting phenix.real_space_refine
on Sat Aug 23 17:19:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uen_20754/08_2025/6uen_20754.map"
  }
  resolution = 3.67
  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=   0.000 sd=   0.014
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      75      5.16       5
     C    8726      2.51       5
     N    2342      2.21       5
     O    2562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13705
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 11352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1392, 11352
          Classifications: {'peptide': 1392}
          Link IDs: {'PTRANS': 47, 'TRANS': 1344}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 460
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 1, 'TRANS': 58}
    Chain: "C"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 423
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
    Chain: "D"
      Number of atoms: 585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 585
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 885
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 2, 'TRANS': 111}
  Time building chain proxies: 2.94, per 1000 atoms: 0.21
  Number of scatterers: 13705
  At special positions: 0
  Unit cell: (109.398, 140.422, 102.867, 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      75     16.00
     O    2562      8.00
     N    2342      7.00
     C    8726      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: 1.10
  Conformation dependent library (CDL) restraints added in 613.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3250

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 8 sheets defined
      62.0% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 3.887A  pdb=" N   TYR A  34 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 4.041A  pdb=" N   LEU A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 64
      removed outlier: 3.576A  pdb=" N   LEU A  64 " --> pdb=" O   ASN A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 76
      removed outlier: 3.669A  pdb=" N   GLN A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 93
      removed outlier: 3.580A  pdb=" N   PHE A  87 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 120
      removed outlier: 3.840A  pdb=" N   GLN A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 175 through 183
    Processing helix  chain 'A' and resid 187 through 197
      removed outlier: 3.818A  pdb=" N   LEU A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 228
      removed outlier: 3.711A  pdb=" N   ILE A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
    Processing helix  chain 'A' and resid 306 through 324
    Processing helix  chain 'A' and resid 327 through 335
      removed outlier: 3.984A  pdb=" N   ILE A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 4.129A  pdb=" N   ILE A 339 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 379
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.567A  pdb=" N   ASP A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LYS A 386 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 382 through 386'
    Processing helix  chain 'A' and resid 389 through 395
      removed outlier: 4.331A  pdb=" N   ILE A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY A 395 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 413
      removed outlier: 4.155A  pdb=" N   LEU A 400 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 421
    Processing helix  chain 'A' and resid 424 through 429
      removed outlier: 4.517A  pdb=" N   PHE A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 448
      removed outlier: 3.569A  pdb=" N   MET A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASP A 441 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ALA A 442 " --> pdb=" O   GLN A 438 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   VAL A 443 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 478
    Processing helix  chain 'A' and resid 490 through 499
      removed outlier: 4.023A  pdb=" N   TYR A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU A 499 " --> pdb=" O   THR A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
      removed outlier: 4.105A  pdb=" N   LEU A 513 " --> pdb=" O   THR A 509 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
      removed outlier: 3.924A  pdb=" N   ILE A 536 " --> pdb=" O   ASP A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 553
      removed outlier: 5.403A  pdb=" N   TRP A 550 " --> pdb=" O   ASN A 547 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE A 553 " --> pdb=" O   TRP A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 570
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 595 through 604
      removed outlier: 4.029A  pdb=" N   VAL A 602 " --> pdb=" O   TYR A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 651
    Processing helix  chain 'A' and resid 652 through 655
    Processing helix  chain 'A' and resid 709 through 724
      removed outlier: 3.553A  pdb=" N   SER A 713 " --> pdb=" O   ARG A 709 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   CYS A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL A 719 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU A 720 " --> pdb=" O   CYS A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 737
      removed outlier: 3.509A  pdb=" N   LEU A 735 " --> pdb=" O   SER A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 759 through 763
      removed outlier: 3.557A  pdb=" N   ASN A 762 " --> pdb=" O   ASP A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 801
      removed outlier: 3.819A  pdb=" N   TRP A 785 " --> pdb=" O   CYS A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 852
    Processing helix  chain 'A' and resid 882 through 887
      removed outlier: 3.784A  pdb=" N   LYS A 886 " --> pdb=" O   ALA A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 919
    Processing helix  chain 'A' and resid 922 through 939
      removed outlier: 3.786A  pdb=" N   TRP A 932 " --> pdb=" O   PHE A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 966
    Processing helix  chain 'A' and resid 970 through 980
    Processing helix  chain 'A' and resid 982 through 986
    Processing helix  chain 'A' and resid 1004 through 1017
    Processing helix  chain 'A' and resid 1034 through 1045
      removed outlier: 3.562A  pdb=" N   THR A1045 " --> pdb=" O   THR A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1060
    Processing helix  chain 'A' and resid 1072 through 1087
      removed outlier: 3.507A  pdb=" N   ILE A1076 " --> pdb=" O   ILE A1072 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   LEU A1079 " --> pdb=" O   GLU A1075 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   ALA A1080 " --> pdb=" O   ILE A1076 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A1087 " --> pdb=" O   GLU A1083 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1099
    Processing helix  chain 'A' and resid 1099 through 1111
      removed outlier: 3.828A  pdb=" N   THR A1103 " --> pdb=" O   HIS A1099 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU A1104 " --> pdb=" O   TYR A1100 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   MET A1111 " --> pdb=" O   LEU A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1129
    Processing helix  chain 'A' and resid 1131 through 1142
      removed outlier: 3.630A  pdb=" N   ILE A1141 " --> pdb=" O   ILE A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1153
    Processing helix  chain 'A' and resid 1158 through 1180
      removed outlier: 3.712A  pdb=" N   ILE A1162 " --> pdb=" O   ASP A1158 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LEU A1176 " --> pdb=" O   ASN A1172 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ILE A1177 " --> pdb=" O   ILE A1173 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG A1178 " --> pdb=" O   THR A1174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1198 through 1212
      removed outlier: 3.864A  pdb=" N   TRP A1211 " --> pdb=" O   ARG A1207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1223 through 1228
    Processing helix  chain 'A' and resid 1282 through 1299
    Processing helix  chain 'A' and resid 1304 through 1317
    Processing helix  chain 'A' and resid 1320 through 1326
      removed outlier: 3.733A  pdb=" N   LYS A1326 " --> pdb=" O   GLU A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1359
      removed outlier: 3.916A  pdb=" N   THR A1358 " --> pdb=" O   PRO A1354 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR A1359 " --> pdb=" O   ALA A1355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1354 through 1359'
    Processing helix  chain 'A' and resid 1365 through 1375
      removed outlier: 3.677A  pdb=" N   ASN A1369 " --> pdb=" O   THR A1365 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE A1371 " --> pdb=" O   PRO A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1385 through 1404
      removed outlier: 3.758A  pdb=" N   ILE A1389 " --> pdb=" O   PHE A1385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1443
      removed outlier: 3.599A  pdb=" N   GLN A1443 " --> pdb=" O   VAL A1439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1452 through 1460
      removed outlier: 4.089A  pdb=" N   PHE A1460 " --> pdb=" O   TYR A1456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
    Processing helix  chain 'B' and resid 157 through 165
      removed outlier: 3.630A  pdb=" N   SER B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ARG B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASP B 164 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 172
    Processing helix  chain 'B' and resid 174 through 187
      removed outlier: 3.807A  pdb=" N   ILE B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 158
      removed outlier: 3.774A  pdb=" N   ALA C 157 " --> pdb=" O   VAL C 153 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   GLY C 158 " --> pdb=" O   VAL C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 182
      removed outlier: 4.726A  pdb=" N   ASP C 164 " --> pdb=" O   THR C 160 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ARG C 167 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 158
    Processing helix  chain 'D' and resid 171 through 202
      removed outlier: 3.507A  pdb=" N   GLU D 175 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ARG D 191 " --> pdb=" O   MET D 187 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU D 192 " --> pdb=" O   THR D 188 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   MET D 195 " --> pdb=" O   ARG D 191 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 152
      removed outlier: 3.596A  pdb=" N   LEU E 152 " --> pdb=" O   MET E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 183
      removed outlier: 3.527A  pdb=" N   MET E 177 " --> pdb=" O   LEU E 173 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 199
      removed outlier: 3.512A  pdb=" N   ALA E 196 " --> pdb=" O   LEU E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 203 through 210
      removed outlier: 3.740A  pdb=" N   ALA E 207 " --> pdb=" O   SER E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 217 through 228
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
      removed outlier: 6.670A  pdb=" N   LYS A  80 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      removed outlier: 9.093A  pdb=" N   VAL A 263 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 631
    Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 808
    Processing sheet with id=AA5, first strand: chain 'A' and resid 867 through 869
      removed outlier: 4.879A  pdb=" N   GLN A 867 " --> pdb=" O   GLN A 874 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   GLN A 874 " --> pdb=" O   GLN A 867 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET A 869 " --> pdb=" O   THR A 872 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ILE A 873 " --> pdb=" O   TYR A 880 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1229 through 1231
      removed outlier: 3.533A  pdb=" N   ILE A1413 " --> pdb=" O   ASP A1229 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1272
    Processing sheet with id=AA8, first strand: chain 'E' and resid 158 through 159
      removed outlier: 3.836A  pdb=" N   GLY E 158 " --> pdb=" O   ARG E 167 " (cutoff:3.500A)

    730 hydrogen bonds defined for protein.
    2118 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: 2.40

  Time building geometry restraints manager: 1.50 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: 4468
        1.34 -     1.46: 2345
        1.46 -     1.58: 7007
        1.58 -     1.69: 0
        1.69 -     1.81: 127
  Bond restraints: 13947
  Sorted by residual:
  bond pdb=" C   GLY A 430 "
       pdb=" N   HIS A 431 "
    ideal  model  delta    sigma   weight residual
    1.331  1.301  0.030 2.07e-02 2.33e+03 2.11e+00
  bond pdb=" CB  ILE A 428 "
       pdb=" CG2 ILE A 428 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU A 131 "
       pdb=" CD1 LEU A 131 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" CB  ILE A 787 "
       pdb=" CG2 ILE A 787 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.13e+00
  bond pdb=" CB  LEU A 313 "
       pdb=" CG  LEU A 313 "
    ideal  model  delta    sigma   weight residual
    1.530  1.509  0.021 2.00e-02 2.50e+03 1.10e+00
  ... (remaining 13942 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 18147
        1.51 -     3.01: 583
        3.01 -     4.52: 94
        4.52 -     6.02: 14
        6.02 -     7.53: 6
  Bond angle restraints: 18844
  Sorted by residual:
  angle pdb=" C   MET A 628 "
        pdb=" N   PHE A 629 "
        pdb=" CA  PHE A 629 "
      ideal   model   delta    sigma   weight residual
     122.74  117.49    5.25 1.82e+00 3.02e-01 8.33e+00
  angle pdb=" CA  TRP A 287 "
        pdb=" CB  TRP A 287 "
        pdb=" CG  TRP A 287 "
      ideal   model   delta    sigma   weight residual
     113.60  119.01   -5.41 1.90e+00 2.77e-01 8.11e+00
  angle pdb=" N   GLN A 831 "
        pdb=" CA  GLN A 831 "
        pdb=" C   GLN A 831 "
      ideal   model   delta    sigma   weight residual
     113.72  109.61    4.11 1.52e+00 4.33e-01 7.32e+00
  angle pdb=" N   GLN A 831 "
        pdb=" CA  GLN A 831 "
        pdb=" CB  GLN A 831 "
      ideal   model   delta    sigma   weight residual
     113.65  109.91    3.74 1.47e+00 4.63e-01 6.48e+00
  angle pdb=" C   ASN A1113 "
        pdb=" N   ILE A1114 "
        pdb=" CA  ILE A1114 "
      ideal   model   delta    sigma   weight residual
     120.69  124.18   -3.49 1.46e+00 4.69e-01 5.70e+00
  ... (remaining 18839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7639
       17.92 -    35.84: 758
       35.84 -    53.76: 118
       53.76 -    71.68: 18
       71.68 -    89.60: 11
  Dihedral angle restraints: 8544
    sinusoidal: 3538
      harmonic: 5006
  Sorted by residual:
  dihedral pdb=" CA  PHE A 244 "
           pdb=" C   PHE A 244 "
           pdb=" N   ILE A 245 "
           pdb=" CA  ILE A 245 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.22   18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ASN A1139 "
           pdb=" C   ASN A1139 "
           pdb=" N   LEU A1140 "
           pdb=" CA  LEU A1140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.29   18.71     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  GLN A 831 "
           pdb=" C   GLN A 831 "
           pdb=" N   ALA A 832 "
           pdb=" CA  ALA A 832 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.58   17.42     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 8541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1419
       0.037 -    0.074: 566
       0.074 -    0.112: 157
       0.112 -    0.149: 30
       0.149 -    0.186: 3
  Chirality restraints: 2175
  Sorted by residual:
  chirality pdb=" CB  VAL A 379 "
            pdb=" CA  VAL A 379 "
            pdb=" CG1 VAL A 379 "
            pdb=" CG2 VAL A 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.66e-01
  chirality pdb=" CB  THR A 745 "
            pdb=" CA  THR A 745 "
            pdb=" OG1 THR A 745 "
            pdb=" CG2 THR A 745 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  ILE A 817 "
            pdb=" N   ILE A 817 "
            pdb=" C   ILE A 817 "
            pdb=" CB  ILE A 817 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.06e-01
  ... (remaining 2172 not shown)

  Planarity restraints: 2381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 632 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 633 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 633 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 633 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1001 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO A1002 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1002 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1002 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 737 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 738 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 738 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 738 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2378 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 220
        2.67 -     3.23: 13904
        3.23 -     3.78: 19770
        3.78 -     4.34: 26248
        4.34 -     4.90: 44239
  Nonbonded interactions: 104381
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 606 "
            pdb=" O   SER A 728 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OH  TYR A 917 "
            pdb=" O   ARG A 995 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" O   TYR A 752 "
            pdb=" NE2 GLN A 766 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" O   ARG A 555 "
            pdb=" NE2 GLN A 563 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OG1 THR B 160 "
            pdb=" OD1 ASP E 168 "
     model   vdw
     2.241 3.040
  ... (remaining 104376 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 128 through 182)
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.100
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.250
  Find NCS groups from input model:        0.080
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
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      :  0.006   0.039  13947  Z= 0.240
  Angle     :  0.654   7.531  18844  Z= 0.361
  Chirality :  0.043   0.186   2175
  Planarity :  0.004   0.052   2381
  Dihedral  : 14.230  89.605   5294
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.35 %
    Favored  : 92.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.18), residues: 1682
  helix: -0.96 (0.15), residues: 947
  sheet: -0.92 (0.59), residues: 59
  loop : -2.28 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 889 
 TYR   0.018   0.002   TYR A 998 
 PHE   0.020   0.002   PHE A  25 
 TRP   0.018   0.002   TRP A 480 
 HIS   0.007   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (13947)
  covalent geometry    : angle       0.65390 (18844)
  hydrogen bonds       : bond        0.14268 (  730)
  hydrogen bonds       : angle       5.98136 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 297
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.7093 (m-80) cc_final: 0.6080 (m-10)
REVERT: A  197 MET cc_start: 0.9018 (mtp) cc_final: 0.8653 (mtm)
REVERT: A  438 GLN cc_start: 0.8104 (mp10) cc_final: 0.7667 (tm-30)
REVERT: A  580 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7786 (mtt90)
REVERT: A  721 ASP cc_start: 0.8232 (t0) cc_final: 0.7805 (t0)
REVERT: A  824 MET cc_start: 0.5857 (mmm) cc_final: 0.5484 (mpp)
REVERT: A  887 VAL cc_start: 0.9311 (m) cc_final: 0.9062 (p)
REVERT: A  959 LEU cc_start: 0.9128 (mt) cc_final: 0.8870 (mp)
REVERT: A 1017 SER cc_start: 0.9083 (m) cc_final: 0.8852 (p)
REVERT: A 1169 MET cc_start: 0.8778 (mtm) cc_final: 0.8384 (mtm)
REVERT: A 1290 ASP cc_start: 0.7293 (t70) cc_final: 0.6946 (t0)
REVERT: B  161 SER cc_start: 0.8324 (p) cc_final: 0.8083 (p)
REVERT: B  175 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6649 (mt-10)
REVERT: C  141 LYS cc_start: 0.7335 (mttp) cc_final: 0.7022 (mttp)
REVERT: C  177 MET cc_start: 0.5497 (mtp) cc_final: 0.5294 (mmm)
REVERT: D  150 HIS cc_start: 0.6946 (m-70) cc_final: 0.6584 (m-70)
REVERT: E  148 MET cc_start: 0.7261 (ttt) cc_final: 0.7010 (ttm)
REVERT: E  175 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6440 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 297
  average time/residue: 0.1233
  time to fit residues: 53.1355
Evaluate side-chains
  236 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  75 HIS
A 199 HIS
A 228 ASN
A 363 ASN
A 381 HIS
A 556 ASN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 GLN
A 773 HIS
A 930 ASN
A 980 ASN
B 150 HIS
C 150 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119831 restraints weight = 20054.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.121598 restraints weight = 14616.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.122526 restraints weight = 11039.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.122716 restraints weight = 9628.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.123717 restraints weight = 8849.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13947  Z= 0.122
  Angle     :  0.534   8.192  18844  Z= 0.282
  Chirality :  0.039   0.146   2175
  Planarity :  0.004   0.058   2381
  Dihedral  :  4.484  35.415   1849
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.53 %
    Favored  : 85.05 %
  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 aren not related in a simple way.
  whole: -0.48 (0.20), residues: 1682
  helix:  0.66 (0.16), residues: 968
  sheet: -0.28 (0.56), residues: 73
  loop : -1.85 (0.22), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.012   0.001   TYR A 998 
 PHE   0.014   0.001   PHE A1328 
 TRP   0.015   0.001   TRP A 287 
 HIS   0.006   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (13947)
  covalent geometry    : angle       0.53371 (18844)
  hydrogen bonds       : bond        0.04725 (  730)
  hydrogen bonds       : angle       4.26950 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 283
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.6975 (m-80) cc_final: 0.6015 (m-10)
REVERT: A   92 MET cc_start: 0.8866 (mmp) cc_final: 0.8180 (mmp)
REVERT: A  197 MET cc_start: 0.8633 (mtp) cc_final: 0.8399 (mtm)
REVERT: A  360 MET cc_start: 0.8500 (tmm) cc_final: 0.8207 (ppp)
REVERT: A  374 ASN cc_start: 0.8489 (t0) cc_final: 0.7990 (m110)
REVERT: A  427 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7374 (mmm160)
REVERT: A  512 ASP cc_start: 0.8277 (m-30) cc_final: 0.8069 (m-30)
REVERT: A  568 HIS cc_start: 0.7282 (t70) cc_final: 0.6783 (m-70)
REVERT: A  580 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7749 (mtt90)
REVERT: A  816 ASP cc_start: 0.7425 (p0) cc_final: 0.7128 (p0)
REVERT: A  900 ASP cc_start: 0.7501 (m-30) cc_final: 0.7300 (m-30)
REVERT: A 1226 TYR cc_start: 0.9068 (t80) cc_final: 0.8838 (t80)
REVERT: A 1290 ASP cc_start: 0.7568 (t70) cc_final: 0.7183 (t0)
REVERT: A 1359 THR cc_start: 0.9116 (p) cc_final: 0.8708 (p)
REVERT: B  148 MET cc_start: 0.8397 (ttm) cc_final: 0.8004 (mtp)
REVERT: B  161 SER cc_start: 0.8461 (p) cc_final: 0.8238 (p)
REVERT: C  167 ARG cc_start: 0.6040 (ptm-80) cc_final: 0.5617 (ptt180)
REVERT: D  145 ILE cc_start: 0.7640 (mt) cc_final: 0.7426 (mt)
REVERT: D  150 HIS cc_start: 0.6886 (m-70) cc_final: 0.6388 (m-70)
REVERT: E  142 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6588 (mt)
REVERT: E  146 LEU cc_start: 0.8247 (tt) cc_final: 0.8044 (mm)
REVERT: E  148 MET cc_start: 0.7174 (ttt) cc_final: 0.6940 (ttm)
REVERT: E  175 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6283 (pm20)
REVERT: E  180 LYS cc_start: 0.6347 (mtpp) cc_final: 0.5918 (mttt)
REVERT: E  191 ARG cc_start: 0.7129 (ptm160) cc_final: 0.6689 (tmm-80)
REVERT: E  206 MET cc_start: 0.6535 (tpt) cc_final: 0.6078 (tpt)
  outliers start: 22
  outliers final: 11
  residues processed: 288
  average time/residue: 0.1029
  time to fit residues: 44.8653
Evaluate side-chains
  254 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 242
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  949 ASN
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1396 MET
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  150 HIS
Chi-restraints excluded: chain E residue  160 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 166 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0770
   chunk 58 optimal weight:    9.9990
   chunk 121 optimal weight:    0.0270
   chunk 14 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 153 optimal weight:   30.0000
   chunk 81 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.3398

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 215 ASN
A 448 ASN
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 HIS
E 150 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.152107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.120839 restraints weight = 20354.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.122783 restraints weight = 14192.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124054 restraints weight = 10780.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124269 restraints weight = 8919.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124529 restraints weight = 8540.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13947  Z= 0.115
  Angle     :  0.507   9.159  18844  Z= 0.265
  Chirality :  0.038   0.136   2175
  Planarity :  0.003   0.058   2381
  Dihedral  :  4.250  34.448   1849
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.40 %
    Favored  : 82.28 %
  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 aren not related in a simple way.
  whole:  0.24 (0.20), residues: 1682
  helix:  1.29 (0.17), residues: 967
  sheet: -0.15 (0.58), residues: 72
  loop : -1.61 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 462 
 TYR   0.011   0.001   TYR A 998 
 PHE   0.011   0.001   PHE A1328 
 TRP   0.012   0.001   TRP A 287 
 HIS   0.006   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (13947)
  covalent geometry    : angle       0.50657 (18844)
  hydrogen bonds       : bond        0.04218 (  730)
  hydrogen bonds       : angle       3.97282 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 272
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.6950 (m-80) cc_final: 0.6013 (m-10)
REVERT: A  197 MET cc_start: 0.8715 (mtp) cc_final: 0.8502 (mtm)
REVERT: A  204 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7759 (tt)
REVERT: A  340 MET cc_start: 0.7518 (mtp) cc_final: 0.7300 (mtt)
REVERT: A  360 MET cc_start: 0.8503 (tmm) cc_final: 0.8140 (ppp)
REVERT: A  374 ASN cc_start: 0.8278 (t0) cc_final: 0.8047 (m110)
REVERT: A  512 ASP cc_start: 0.8446 (m-30) cc_final: 0.8187 (m-30)
REVERT: A  568 HIS cc_start: 0.7285 (t70) cc_final: 0.6832 (m-70)
REVERT: A  580 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7734 (mtt90)
REVERT: A  607 LEU cc_start: 0.8970 (mt) cc_final: 0.8740 (mp)
REVERT: A  619 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6533 (tttm)
REVERT: A  722 GLU cc_start: 0.8518 (tp30) cc_final: 0.7894 (mm-30)
REVERT: A  816 ASP cc_start: 0.7496 (p0) cc_final: 0.7175 (p0)
REVERT: A 1046 PHE cc_start: 0.7863 (p90) cc_final: 0.7630 (p90)
REVERT: A 1290 ASP cc_start: 0.7657 (t70) cc_final: 0.7306 (t0)
REVERT: A 1430 ASP cc_start: 0.8352 (m-30) cc_final: 0.8117 (m-30)
REVERT: B  174 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7366 (mmt90)
REVERT: C  167 ARG cc_start: 0.6344 (ptm-80) cc_final: 0.5986 (ptt180)
REVERT: D  150 HIS cc_start: 0.7167 (m-70) cc_final: 0.6647 (m-70)
REVERT: E  142 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6669 (mt)
REVERT: E  146 LEU cc_start: 0.8289 (tt) cc_final: 0.8083 (mm)
REVERT: E  148 MET cc_start: 0.7396 (ttt) cc_final: 0.6998 (ttm)
REVERT: E  163 ARG cc_start: 0.7902 (ptp90) cc_final: 0.7655 (ptp-170)
REVERT: E  175 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6218 (pm20)
REVERT: E  180 LYS cc_start: 0.6716 (mtpp) cc_final: 0.6173 (mttt)
REVERT: E  187 MET cc_start: 0.7952 (ppp) cc_final: 0.7424 (ppp)
REVERT: E  191 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6959 (tmm-80)
  outliers start: 36
  outliers final: 20
  residues processed: 289
  average time/residue: 0.0992
  time to fit residues: 43.4152
Evaluate side-chains
  264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 242
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1279 GLN
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1396 MET
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  150 HIS
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  171 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 105 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 50 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 116 optimal weight:    0.0670
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 164 optimal weight:   10.0000
   chunk 159 optimal weight:    4.9990
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
A 561 HIS
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 HIS
E 150 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.121814 restraints weight = 20196.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.124496 restraints weight = 13951.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125841 restraints weight = 10269.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.125931 restraints weight = 8497.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126105 restraints weight = 8225.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13947  Z= 0.101
  Angle     :  0.494   8.492  18844  Z= 0.257
  Chirality :  0.038   0.156   2175
  Planarity :  0.003   0.054   2381
  Dihedral  :  4.082  31.514   1849
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.27 %
    Favored  : 80.28 %
  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 aren not related in a simple way.
  whole:  0.60 (0.21), residues: 1682
  helix:  1.60 (0.17), residues: 971
  sheet: -0.07 (0.59), residues: 72
  loop : -1.48 (0.23), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 174 
 TYR   0.011   0.001   TYR A 917 
 PHE   0.010   0.001   PHE A  87 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.013   0.001   HIS E 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (13947)
  covalent geometry    : angle       0.49437 (18844)
  hydrogen bonds       : bond        0.03777 (  730)
  hydrogen bonds       : angle       3.83556 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 257
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.6947 (m-80) cc_final: 0.5981 (m-10)
REVERT: A  197 MET cc_start: 0.8714 (mtp) cc_final: 0.8468 (mtm)
REVERT: A  360 MET cc_start: 0.8433 (tmm) cc_final: 0.8042 (ppp)
REVERT: A  374 ASN cc_start: 0.8256 (t0) cc_final: 0.8042 (m110)
REVERT: A  453 TYR cc_start: 0.8104 (m-80) cc_final: 0.7586 (m-10)
REVERT: A  460 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7760 (mtm)
REVERT: A  512 ASP cc_start: 0.8367 (m-30) cc_final: 0.8084 (m-30)
REVERT: A  568 HIS cc_start: 0.7259 (t70) cc_final: 0.6818 (m-70)
REVERT: A  580 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7697 (mtt90)
REVERT: A  619 LYS cc_start: 0.7018 (ttmt) cc_final: 0.6302 (tttm)
REVERT: A  646 MET cc_start: 0.8625 (mmm) cc_final: 0.8196 (mmm)
REVERT: A  816 ASP cc_start: 0.7453 (p0) cc_final: 0.7161 (p0)
REVERT: A 1309 MET cc_start: 0.8548 (tpp) cc_final: 0.8287 (mmt)
REVERT: A 1359 THR cc_start: 0.9296 (p) cc_final: 0.8853 (p)
REVERT: C  137 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6592 (mtp85)
REVERT: C  167 ARG cc_start: 0.6244 (ptm-80) cc_final: 0.5770 (ptt180)
REVERT: E  148 MET cc_start: 0.7504 (ttt) cc_final: 0.7244 (ttm)
REVERT: E  175 GLU cc_start: 0.6548 (mm-30) cc_final: 0.5716 (pm20)
REVERT: E  180 LYS cc_start: 0.6589 (mtpp) cc_final: 0.6049 (mttt)
REVERT: E  187 MET cc_start: 0.8062 (ppp) cc_final: 0.7590 (ppp)
REVERT: E  191 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6871 (tmm-80)
  outliers start: 38
  outliers final: 23
  residues processed: 276
  average time/residue: 0.0992
  time to fit residues: 41.9208
Evaluate side-chains
  264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1279 GLN
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1396 MET
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain E residue  150 HIS
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  171 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 160 optimal weight:    7.9990
   chunk 128 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 158 optimal weight:    0.7980
   chunk 146 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0030
   chunk 88 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 132 optimal weight:    0.9990
   chunk 87 optimal weight:    9.9990
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
A 448 ASN
A 604 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 GLN
C 150 HIS
D 150 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.122400 restraints weight = 20179.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124771 restraints weight = 13880.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125701 restraints weight = 10394.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125798 restraints weight = 9133.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.127152 restraints weight = 8587.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13947  Z= 0.106
  Angle     :  0.511  14.527  18844  Z= 0.261
  Chirality :  0.038   0.260   2175
  Planarity :  0.003   0.053   2381
  Dihedral  :  4.007  31.796   1849
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.36 %
    Favored  : 78.87 %
  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 aren not related in a simple way.
  whole:  0.77 (0.21), residues: 1682
  helix:  1.73 (0.17), residues: 972
  sheet: -0.09 (0.54), residues: 83
  loop : -1.40 (0.24), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 174 
 TYR   0.012   0.001   TYR A 917 
 PHE   0.010   0.001   PHE A 424 
 TRP   0.010   0.001   TRP A 287 
 HIS   0.012   0.001   HIS E 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (13947)
  covalent geometry    : angle       0.51084 (18844)
  hydrogen bonds       : bond        0.03805 (  730)
  hydrogen bonds       : angle       3.76050 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 255
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.6726 (m-80) cc_final: 0.5702 (m-10)
REVERT: A  197 MET cc_start: 0.8692 (mtp) cc_final: 0.8491 (mtm)
REVERT: A  204 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7938 (tt)
REVERT: A  360 MET cc_start: 0.8429 (tmm) cc_final: 0.8014 (ppp)
REVERT: A  453 TYR cc_start: 0.8139 (m-80) cc_final: 0.7642 (m-10)
REVERT: A  568 HIS cc_start: 0.7155 (t70) cc_final: 0.6721 (m-70)
REVERT: A  580 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7660 (mtt90)
REVERT: A  619 LYS cc_start: 0.6997 (ttmt) cc_final: 0.6291 (tttm)
REVERT: A  816 ASP cc_start: 0.7486 (p0) cc_final: 0.7203 (p0)
REVERT: A  898 LEU cc_start: 0.7472 (tp) cc_final: 0.7145 (tt)
REVERT: A 1168 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7033 (ttp)
REVERT: A 1182 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7730 (pp)
REVERT: A 1309 MET cc_start: 0.8690 (tpp) cc_final: 0.8329 (mmt)
REVERT: A 1359 THR cc_start: 0.9149 (p) cc_final: 0.8681 (p)
REVERT: A 1436 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: A 1449 ASP cc_start: 0.8513 (t0) cc_final: 0.7967 (t0)
REVERT: B  152 LEU cc_start: 0.8596 (tt) cc_final: 0.8328 (tp)
REVERT: C  137 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6621 (mtp85)
REVERT: C  141 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6746 (mttt)
REVERT: C  167 ARG cc_start: 0.6288 (ptm-80) cc_final: 0.5868 (ptt180)
REVERT: E  148 MET cc_start: 0.7897 (ttt) cc_final: 0.7587 (ttm)
REVERT: E  150 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (m-70)
REVERT: E  175 GLU cc_start: 0.6755 (mm-30) cc_final: 0.5891 (pm20)
REVERT: E  180 LYS cc_start: 0.6559 (mtpp) cc_final: 0.6019 (mttt)
REVERT: E  187 MET cc_start: 0.8040 (ppp) cc_final: 0.7610 (ppp)
REVERT: E  191 ARG cc_start: 0.7163 (ptm160) cc_final: 0.6885 (tmm-80)
  outliers start: 43
  outliers final: 26
  residues processed: 276
  average time/residue: 0.0992
  time to fit residues: 41.7554
Evaluate side-chains
  267 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 236
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain A residue  948 ASN
Chi-restraints excluded: chain A residue 1076 ILE
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1179 ILE
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1396 MET
Chi-restraints excluded: chain A residue 1436 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  150 HIS
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain E residue  150 HIS
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  171 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.118853 restraints weight = 20332.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119679 restraints weight = 14025.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.120730 restraints weight = 11389.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.121021 restraints weight = 9790.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.122690 restraints weight = 8936.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13947  Z= 0.155
  Angle     :  0.548  13.551  18844  Z= 0.286
  Chirality :  0.040   0.147   2175
  Planarity :  0.004   0.057   2381
  Dihedral  :  4.205  36.813   1849
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.46 %
    Favored  : 77.51 %
  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 aren not related in a simple way.
  whole:  0.63 (0.20), residues: 1682
  helix:  1.59 (0.17), residues: 974
  sheet:  0.04 (0.58), residues: 72
  loop : -1.44 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.015   0.001   TYR A 998 
 PHE   0.015   0.002   PHE A  25 
 TRP   0.011   0.002   TRP A 480 
 HIS   0.022   0.001   HIS D 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13947)
  covalent geometry    : angle       0.54818 (18844)
  hydrogen bonds       : bond        0.04658 (  730)
  hydrogen bonds       : angle       3.92866 ( 2118)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 240
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.6770 (m-80) cc_final: 0.5702 (m-10)
REVERT: A  197 MET cc_start: 0.8792 (mtp) cc_final: 0.8540 (mtm)
REVERT: A  204 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7932 (tt)
REVERT: A  360 MET cc_start: 0.8516 (tmm) cc_final: 0.8092 (ppp)
REVERT: A  453 TYR cc_start: 0.8299 (m-80) cc_final: 0.7933 (m-10)
REVERT: A  514 ILE cc_start: 0.8645 (mt) cc_final: 0.8438 (mt)
REVERT: A  568 HIS cc_start: 0.7183 (t70) cc_final: 0.6743 (m-70)
REVERT: A  580 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7703 (mtt90)
REVERT: A  646 MET cc_start: 0.8675 (mmm) cc_final: 0.8352 (mmm)
REVERT: A  700 ASP cc_start: 0.8475 (t0) cc_final: 0.8236 (t0)
REVERT: A  804 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (tt)
REVERT: A  816 ASP cc_start: 0.7501 (p0) cc_final: 0.7171 (p0)
REVERT: A  898 LEU cc_start: 0.7453 (tp) cc_final: 0.7087 (tt)
REVERT: A 1109 ASP cc_start: 0.6986 (m-30) cc_final: 0.6692 (m-30)
REVERT: A 1168 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7125 (ttp)
REVERT: A 1182 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7778 (pp)
REVERT: A 1309 MET cc_start: 0.8789 (tpp) cc_final: 0.8397 (mmt)
REVERT: A 1359 THR cc_start: 0.9200 (p) cc_final: 0.8806 (p)
REVERT: A 1436 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8921 (tt)
REVERT: A 1449 ASP cc_start: 0.8539 (t0) cc_final: 0.7987 (t0)
REVERT: B  152 LEU cc_start: 0.8633 (tt) cc_final: 0.8421 (tp)
REVERT: B  161 SER cc_start: 0.9186 (t) cc_final: 0.8860 (p)
REVERT: C  141 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6963 (mttt)
REVERT: C  167 ARG cc_start: 0.6305 (ptm-80) cc_final: 0.5794 (ptt180)
REVERT: E  148 MET cc_start: 0.8042 (ttt) cc_final: 0.7622 (ttm)
REVERT: E  163 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7673 (ptp-170)
REVERT: E  175 GLU cc_start: 0.6675 (mm-30) cc_final: 0.5716 (pm20)
REVERT: E  180 LYS cc_start: 0.6577 (mtpp) cc_final: 0.6002 (mttt)
REVERT: E  191 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6921 (tmm-80)
  outliers start: 47
  outliers final: 31
  residues processed: 265
  average time/residue: 0.0996
  time to fit residues: 40.5151
Evaluate side-chains
  264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 228
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  743 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain A residue  948 ASN
Chi-restraints excluded: chain A residue 1076 ILE
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1279 GLN
Chi-restraints excluded: chain A residue 1336 TYR
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1436 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain E residue  150 HIS
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  171 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 67.73 > 50:
  distance: 60 - 62:  25.272
  distance: 62 - 63:  34.568
  distance: 63 - 64:  33.804
  distance: 63 - 66:  23.574
  distance: 64 - 65:  13.845
  distance: 64 - 70:  12.548
  distance: 66 - 67:  20.400
  distance: 67 - 68:  32.094
  distance: 67 - 69:  18.465
  distance: 70 - 71:  44.897
  distance: 71 - 72:  11.890
  distance: 71 - 74:  15.773
  distance: 72 - 73:  10.043
  distance: 72 - 77:  14.212
  distance: 73 - 107:  47.362
  distance: 74 - 75:  14.883
  distance: 74 - 76:  20.805
  distance: 77 - 78:  16.014
  distance: 78 - 79:  17.475
  distance: 78 - 81:  18.012
  distance: 79 - 80:  37.148
  distance: 79 - 89:  40.052
  distance: 80 - 112:  19.553
  distance: 81 - 82:  20.817
  distance: 82 - 83:   6.910
  distance: 82 - 84:   7.333
  distance: 83 - 85:   3.154
  distance: 84 - 86:   5.965
  distance: 85 - 87:   4.815
  distance: 86 - 87:   9.610
  distance: 87 - 88:   3.338
  distance: 89 - 90:  23.537
  distance: 90 - 91:  41.338
  distance: 90 - 93:  20.396
  distance: 91 - 92:  13.413
  distance: 91 - 98:  16.937
  distance: 93 - 94:  34.904
  distance: 94 - 95:  25.072
  distance: 95 - 96:  10.824
  distance: 95 - 97:   6.612
  distance: 98 - 99:  44.576
  distance: 99 - 100:  14.846
  distance: 99 - 102:  23.867
  distance: 100 - 101:  13.829
  distance: 100 - 107:  15.617
  distance: 102 - 103:  37.359
  distance: 103 - 104:  39.236
  distance: 104 - 105:  12.361
  distance: 105 - 106:  40.217
  distance: 107 - 108:  26.096
  distance: 108 - 109:   9.128
  distance: 108 - 111:  28.481
  distance: 109 - 110:  18.417
  distance: 109 - 112:  12.231
  distance: 112 - 113:  35.144
  distance: 113 - 114:  28.108
  distance: 113 - 116:  32.186
  distance: 114 - 115:   5.225
  distance: 114 - 121:  20.748
  distance: 116 - 117:  26.027
  distance: 117 - 118:  25.031
  distance: 118 - 119:  40.392
  distance: 119 - 120:  13.920
  distance: 121 - 122:  27.499
  distance: 122 - 123:   9.485
  distance: 122 - 125:  20.036
  distance: 123 - 124:  36.898
  distance: 123 - 130:  15.192
  distance: 125 - 126:  14.069
  distance: 126 - 127:  13.053
  distance: 127 - 128:  36.108
  distance: 128 - 129:  14.399
  distance: 130 - 131:  20.325
  distance: 131 - 132:  44.935
  distance: 131 - 134:  12.237
  distance: 132 - 133:  44.824
  distance: 132 - 138:  67.730
  distance: 134 - 135:  46.286
  distance: 135 - 136:  17.418
  distance: 135 - 137:  32.515
  distance: 138 - 139:  56.504
  distance: 139 - 140:  13.616
  distance: 139 - 142:  25.309
  distance: 140 - 141:  27.880
  distance: 140 - 149:  26.132
  distance: 142 - 143:  16.011
  distance: 143 - 144:  18.775
  distance: 143 - 145:  30.396
  distance: 144 - 146:  10.023
  distance: 145 - 147:  12.553
  distance: 146 - 148:  17.844
  distance: 147 - 148:  25.262