Starting phenix.real_space_refine
on Wed Mar 12 07:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pzc_20534/03_2025/6pzc_20534_neut.cif"
  }
  resolution = 4.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      20      5.16       5
     C    4723      2.51       5
     N    1354      2.21       5
     O    1359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7456
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "H"
      Number of atoms: 7456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1173, 7456
          Classifications: {'peptide': 1173}
          Incomplete info: {'truncation_to_alanine': 541}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 1134}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1772
          Unresolved non-hydrogen angles: 2243
          Unresolved non-hydrogen dihedrals: 1389
          Unresolved non-hydrogen chiralities: 234
          Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 35, 'PHE:plan': 21, 'GLU:plan': 36, 'ARG:plan': 31}
          Unresolved non-hydrogen planarities: 807
  Time building chain proxies: 4.62, per 1000 atoms: 0.62
  Number of scatterers: 7456
  At special positions: 0
  Unit cell: (84.28, 94.6, 135.88, 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      20     16.00
     O    1359      8.00
     N    1354      7.00
     C    4723      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: 2.07
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2226

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 5 sheets defined
      66.7% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'H' and resid 223 through 230
    Processing helix  chain 'H' and resid 231 through 243
      removed outlier: 4.275A  pdb=" N   ALA H 235 " --> pdb=" O   TRP H 231 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE H 236 " --> pdb=" O   TRP H 232 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LYS H 242 " --> pdb=" O   LYS H 238 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 258 through 274
      removed outlier: 3.608A  pdb=" N   ASN H 262 " --> pdb=" O   ARG H 258 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 283 through 327
      removed outlier: 3.521A  pdb=" N   ARG H 289 " --> pdb=" O   ARG H 285 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   HIS H 293 " --> pdb=" O   ARG H 289 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ARG H 297 " --> pdb=" O   HIS H 293 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ARG H 298 " --> pdb=" O   ALA H 294 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA H 315 " --> pdb=" O   LEU H 311 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLY H 316 " --> pdb=" O   LEU H 312 " (cutoff:3.500A)
      Proline residue:  H 317  - end of helix
    Processing helix  chain 'H' and resid 347 through 352
    Processing helix  chain 'H' and resid 354 through 400
      removed outlier: 3.951A  pdb=" N   LEU H 368 " --> pdb=" O   LEU H 364 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU H 373 " --> pdb=" O   GLN H 369 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   GLN H 374 " --> pdb=" O   ARG H 370 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR H 378 " --> pdb=" O   GLN H 374 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA H 380 " --> pdb=" O   SER H 376 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   ASN H 386 " --> pdb=" O   GLU H 382 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLY H 389 " --> pdb=" O   ILE H 385 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA H 390 " --> pdb=" O   ASN H 386 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LYS H 394 " --> pdb=" O   ALA H 390 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 413 through 423
      removed outlier: 3.896A  pdb=" N   LEU H 420 " --> pdb=" O   GLN H 416 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 423 through 454
      Proline residue:  H 436  - end of helix
      removed outlier: 3.851A  pdb=" N   TRP H 439 " --> pdb=" O   CYS H 435 " (cutoff:3.500A)
      Proline residue:  H 442  - end of helix
    Processing helix  chain 'H' and resid 457 through 471
      removed outlier: 3.831A  pdb=" N   ALA H 465 " --> pdb=" O   LEU H 461 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   VAL H 466 " --> pdb=" O   ILE H 462 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ILE H 467 " --> pdb=" O   GLY H 463 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA H 471 " --> pdb=" O   ILE H 467 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 471 through 505
      removed outlier: 3.809A  pdb=" N   TYR H 475 " --> pdb=" O   ALA H 471 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR H 479 " --> pdb=" O   TYR H 475 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS H 480 " --> pdb=" O   PHE H 476 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   GLU H 494 " --> pdb=" O   GLU H 490 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ARG H 495 " --> pdb=" O   HIS H 491 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY H 505 " --> pdb=" O   GLU H 501 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 505 through 512
    Processing helix  chain 'H' and resid 514 through 564
      removed outlier: 3.684A  pdb=" N   PHE H 518 " --> pdb=" O   TRP H 514 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL H 522 " --> pdb=" O   PHE H 518 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS H 528 " --> pdb=" O   VAL H 524 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA H 535 " --> pdb=" O   THR H 531 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE H 542 " --> pdb=" O   VAL H 538 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER H 543 " --> pdb=" O   TYR H 539 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE H 544 " --> pdb=" O   THR H 540 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE H 550 " --> pdb=" O   MET H 546 " (cutoff:3.500A)
      Proline residue:  H 551  - end of helix
      removed outlier: 3.643A  pdb=" N   ILE H 557 " --> pdb=" O   ALA H 553 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 572 through 591
      removed outlier: 3.529A  pdb=" N   LEU H 580 " --> pdb=" O   ALA H 576 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL H 587 " --> pdb=" O   PHE H 583 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   THR H 588 " --> pdb=" O   HIS H 584 " (cutoff:3.500A)
      Proline residue:  H 589  - end of helix
    Processing helix  chain 'H' and resid 592 through 615
      removed outlier: 3.838A  pdb=" N   GLN H 608 " --> pdb=" O   LEU H 604 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE H 613 " --> pdb=" O   LYS H 609 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 720 through 728
      removed outlier: 3.549A  pdb=" N   GLY H 728 " --> pdb=" O   LEU H 724 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 783 through 790
    Processing helix  chain 'H' and resid 795 through 807
      removed outlier: 4.756A  pdb=" N   ALA H 805 " --> pdb=" O   MET H 801 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 808 through 815
    Processing helix  chain 'H' and resid 817 through 821
    Processing helix  chain 'H' and resid 834 through 846
    Processing helix  chain 'H' and resid 855 through 860
      removed outlier: 3.928A  pdb=" N   ALA H 859 " --> pdb=" O   ASP H 855 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 861 through 879
    Processing helix  chain 'H' and resid 918 through 923
      removed outlier: 3.997A  pdb=" N   CYS H 922 " --> pdb=" O   GLN H 918 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 996 through 1004
      removed outlier: 3.993A  pdb=" N   ALA H1000 " --> pdb=" O   ILE H 996 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   CYS H1001 " --> pdb=" O   PRO H 997 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1009 through 1044
      removed outlier: 3.819A  pdb=" N   GLN H1020 " --> pdb=" O   LEU H1016 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS H1024 " --> pdb=" O   GLN H1020 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ALA H1029 " --> pdb=" O   MET H1025 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS H1036 " --> pdb=" O   TYR H1032 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   THR H1038 " --> pdb=" O   LEU H1034 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1060 through 1107
      removed outlier: 3.741A  pdb=" N   MET H1066 " --> pdb=" O   SER H1062 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL H1067 " --> pdb=" O   VAL H1063 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY H1075 " --> pdb=" O   LEU H1071 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE H1076 " --> pdb=" O   CYS H1072 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU H1080 " --> pdb=" O   ILE H1076 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   VAL H1081 " --> pdb=" O   VAL H1077 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL H1086 " --> pdb=" O   THR H1082 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU H1087 " --> pdb=" O   SER H1083 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU H1107 " --> pdb=" O   ASN H1103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1109 through 1116
      removed outlier: 3.661A  pdb=" N   PHE H1113 " --> pdb=" O   PRO H1109 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1117 through 1135
      removed outlier: 3.608A  pdb=" N   ILE H1121 " --> pdb=" O   PRO H1117 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG H1124 " --> pdb=" O   SER H1120 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER H1127 " --> pdb=" O   ASN H1123 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ASP H1128 " --> pdb=" O   ARG H1124 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   CYS H1129 " --> pdb=" O   PHE H1125 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1136 through 1161
      removed outlier: 3.774A  pdb=" N   LEU H1140 " --> pdb=" O   ILE H1136 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LEU H1148 " --> pdb=" O   SER H1144 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU H1149 " --> pdb=" O   ARG H1145 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU H1154 " --> pdb=" O   CYS H1150 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1164 through 1195
      Proline residue:  H1170  - end of helix
      removed outlier: 3.606A  pdb=" N   VAL H1173 " --> pdb=" O   LEU H1169 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL H1174 " --> pdb=" O   PRO H1170 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   VAL H1184 " --> pdb=" O   LYS H1180 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA H1185 " --> pdb=" O   TYR H1181 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG H1187 " --> pdb=" O   ARG H1183 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1196 through 1210
      removed outlier: 3.720A  pdb=" N   LEU H1200 " --> pdb=" O   THR H1196 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1210 through 1218
      removed outlier: 3.557A  pdb=" N   ILE H1214 " --> pdb=" O   GLY H1210 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1219 through 1267
      removed outlier: 3.613A  pdb=" N   TYR H1230 " --> pdb=" O   LYS H1226 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   SER H1233 " --> pdb=" O   GLU H1229 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   GLU H1249 " --> pdb=" O   ASN H1245 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE H1255 " --> pdb=" O   CYS H1251 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1268 through 1271
    Processing helix  chain 'H' and resid 1278 through 1289
      removed outlier: 3.971A  pdb=" N   GLY H1282 " --> pdb=" O   ALA H1278 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU H1283 " --> pdb=" O   GLY H1279 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLY H1284 " --> pdb=" O   LEU H1280 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1290 through 1313
      removed outlier: 4.203A  pdb=" N   TYR H1294 " --> pdb=" O   MET H1290 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL H1299 " --> pdb=" O   LEU H1295 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG H1300 " --> pdb=" O   ASN H1296 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LEU H1302 " --> pdb=" O   MET H1298 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLU H1306 " --> pdb=" O   LEU H1302 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE H1307 " --> pdb=" O   ALA H1303 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA H1311 " --> pdb=" O   ILE H1307 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL H1312 " --> pdb=" O   GLN H1308 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1313 through 1319
      removed outlier: 4.024A  pdb=" N   ALA H1317 " --> pdb=" O   LYS H1313 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1414 through 1419
    Processing helix  chain 'H' and resid 1436 through 1441
    Processing helix  chain 'H' and resid 1450 through 1458
      removed outlier: 3.874A  pdb=" N   LEU H1455 " --> pdb=" O   LEU H1451 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU H1456 " --> pdb=" O   TRP H1452 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1469 through 1472
    Processing helix  chain 'H' and resid 1476 through 1479
      removed outlier: 3.758A  pdb=" N   GLY H1479 " --> pdb=" O   THR H1476 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 1476 through 1479'
    Processing helix  chain 'H' and resid 1485 through 1498
      removed outlier: 3.597A  pdb=" N   CYS H1491 " --> pdb=" O   ARG H1487 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1513 through 1526
    Processing helix  chain 'H' and resid 1539 through 1546
      removed outlier: 3.627A  pdb=" N   THR H1542 " --> pdb=" O   ARG H1539 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER H1545 " --> pdb=" O   THR H1542 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 696 through 703
      removed outlier: 4.978A  pdb=" N   GLY H 684 " --> pdb=" O   ASN H 698 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   THR H 700 " --> pdb=" O   ILE H 682 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE H 682 " --> pdb=" O   THR H 700 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ARG H 702 " --> pdb=" O   GLN H 680 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLN H 680 " --> pdb=" O   ARG H 702 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 1365 through 1368
      removed outlier: 4.539A  pdb=" N   VAL H1365 " --> pdb=" O   ASN H1349 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ASN H1349 " --> pdb=" O   GLY H1401 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLY H1401 " --> pdb=" O   ASN H1349 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER H1351 " --> pdb=" O   PHE H1399 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 1376 through 1377
    Processing sheet with id=AA4, first strand: chain 'H' and resid 1404 through 1405
    Processing sheet with id=AA5, first strand: chain 'H' and resid 1434 through 1435

    503 hydrogen bonds defined for protein.
    1473 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: 2.22

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2219
        1.33 -     1.45: 1277
        1.45 -     1.57: 4065
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 7590
  Sorted by residual:
  bond pdb=" C   GLU H 382 "
       pdb=" N   THR H 383 "
    ideal  model  delta    sigma   weight residual
    1.324  1.218  0.106 2.56e-02 1.53e+03 1.72e+01
  bond pdb=" CB  TYR H 396 "
       pdb=" CG  TYR H 396 "
    ideal  model  delta    sigma   weight residual
    1.512  1.457  0.055 2.20e-02 2.07e+03 6.27e+00
  bond pdb=" N   THR H 383 "
       pdb=" CA  THR H 383 "
    ideal  model  delta    sigma   weight residual
    1.459  1.428  0.030 1.41e-02 5.03e+03 4.63e+00
  bond pdb=" CB  TRP H 739 "
       pdb=" CG  TRP H 739 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.59e+00
  bond pdb=" CB  TRP H1037 "
       pdb=" CG  TRP H1037 "
    ideal  model  delta    sigma   weight residual
    1.498  1.433  0.065 3.10e-02 1.04e+03 4.38e+00
  ... (remaining 7585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 10040
        2.49 -     4.97: 341
        4.97 -     7.46: 53
        7.46 -     9.95: 15
        9.95 -    12.44: 4
  Bond angle restraints: 10453
  Sorted by residual:
  angle pdb=" C   PRO H 281 "
        pdb=" N   GLN H 282 "
        pdb=" CA  GLN H 282 "
      ideal   model   delta    sigma   weight residual
     121.70  131.19   -9.49 1.80e+00 3.09e-01 2.78e+01
  angle pdb=" C   ASN H1338 "
        pdb=" N   TRP H1339 "
        pdb=" CA  TRP H1339 "
      ideal   model   delta    sigma   weight residual
     121.80  132.35  -10.55 2.44e+00 1.68e-01 1.87e+01
  angle pdb=" CA  TRP H1297 "
        pdb=" CB  TRP H1297 "
        pdb=" CG  TRP H1297 "
      ideal   model   delta    sigma   weight residual
     113.60  121.62   -8.02 1.90e+00 2.77e-01 1.78e+01
  angle pdb=" CB  MET H 441 "
        pdb=" CG  MET H 441 "
        pdb=" SD  MET H 441 "
      ideal   model   delta    sigma   weight residual
     112.70  100.26   12.44 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" N   THR H 383 "
        pdb=" CA  THR H 383 "
        pdb=" C   THR H 383 "
      ideal   model   delta    sigma   weight residual
     113.18  107.69    5.49 1.33e+00 5.65e-01 1.70e+01
  ... (remaining 10448 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.06: 4135
       15.06 -    30.12: 234
       30.12 -    45.18: 43
       45.18 -    60.25: 5
       60.25 -    75.31: 2
  Dihedral angle restraints: 4419
    sinusoidal: 1003
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" CA  TRP H1339 "
           pdb=" C   TRP H1339 "
           pdb=" N   PRO H1340 "
           pdb=" CA  PRO H1340 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.26  -52.74     0      5.00e+00 4.00e-02 1.11e+02
  dihedral pdb=" CA  THR H 229 "
           pdb=" C   THR H 229 "
           pdb=" N   TYR H 230 "
           pdb=" CA  TYR H 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.11   38.89     0      5.00e+00 4.00e-02 6.05e+01
  dihedral pdb=" CA  ASN H 223 "
           pdb=" C   ASN H 223 "
           pdb=" N   LEU H 224 "
           pdb=" CA  LEU H 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.66  -33.34     0      5.00e+00 4.00e-02 4.45e+01
  ... (remaining 4416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1103
       0.080 -    0.159: 176
       0.159 -    0.239: 11
       0.239 -    0.319: 4
       0.319 -    0.398: 1
  Chirality restraints: 1295
  Sorted by residual:
  chirality pdb=" CB  ILE H1255 "
            pdb=" CA  ILE H1255 "
            pdb=" CG1 ILE H1255 "
            pdb=" CG2 ILE H1255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" CA  ARG H 826 "
            pdb=" N   ARG H 826 "
            pdb=" C   ARG H 826 "
            pdb=" CB  ARG H 826 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  PHE H1223 "
            pdb=" N   PHE H1223 "
            pdb=" C   PHE H1223 "
            pdb=" CB  PHE H1223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 1292 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H1242 "   -0.022 2.00e-02 2.50e+03   4.46e-02 1.99e+01
        pdb=" C   THR H1242 "    0.077 2.00e-02 2.50e+03
        pdb=" O   THR H1242 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ALA H1243 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H1233 "    0.021 2.00e-02 2.50e+03   4.25e-02 1.81e+01
        pdb=" C   SER H1233 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   SER H1233 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN H1234 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 232 "    0.039 2.00e-02 2.50e+03   2.38e-02 1.41e+01
        pdb=" CG  TRP H 232 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 232 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 232 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 232 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 232 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 232 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 232 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 232 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 232 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 267
        2.69 -     3.24: 8109
        3.24 -     3.79: 12518
        3.79 -     4.35: 14421
        4.35 -     4.90: 21770
  Nonbonded interactions: 57085
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS H 398 "
            pdb=" O   LEU H 614 "
     model   vdw
     2.137 3.120
  nonbonded pdb=" N   ASN H 781 "
            pdb=" OE2 GLU H1206 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" O   LEU H1192 "
            pdb=" OG1 THR H1196 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   LEU H 367 "
            pdb=" OG1 THR H 371 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   LEU H1148 "
            pdb=" OG  SER H1152 "
     model   vdw
     2.247 3.040
  ... (remaining 57080 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.810
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5686
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.106   7590  Z= 0.540
  Angle     :  1.122  12.437  10453  Z= 0.640
  Chirality :  0.058   0.398   1295
  Planarity :  0.010   0.093   1380
  Dihedral  : 11.224  75.307   2193
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  6.96 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.15 (0.18), residues: 1159
  helix: -2.94 (0.13), residues: 712
  sheet: -5.31 (0.48), residues: 19
  loop : -3.97 (0.25), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.005   TRP H 232 
 HIS   0.010   0.004   HIS H 584 
 PHE   0.033   0.004   PHE H 270 
 TYR   0.043   0.004   TYR H 475 
 ARG   0.013   0.002   ARG H 370 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  363 PHE cc_start: 0.7585 (t80) cc_final: 0.7240 (t80)
REVERT: H  367 LEU cc_start: 0.8209 (mt) cc_final: 0.7866 (mt)
REVERT: H  445 ILE cc_start: 0.8403 (mt) cc_final: 0.8018 (mt)
REVERT: H 1121 ILE cc_start: 0.7685 (mt) cc_final: 0.7322 (mp)
REVERT: H 1214 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7121 (mp)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2106
  time to fit residues: 45.3395
Evaluate side-chains
  108 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.0060
   chunk 88 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:   20.0000
   chunk 47 optimal weight:    0.0770
   chunk 91 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.5354

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

Flipped N/Q/H residues before XYZ refinement:
H 234 ASN
H 262 ASN
H 386 ASN
H 444 GLN
H 491 HIS
H 584 HIS
** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.083073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.065044 restraints weight = 30492.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.067024 restraints weight = 20201.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.068346 restraints weight = 14615.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7590  Z= 0.193
  Angle     :  0.639  10.145  10453  Z= 0.340
  Chirality :  0.043   0.217   1295
  Planarity :  0.006   0.094   1380
  Dihedral  :  5.797  46.602   1218
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.38 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.23), residues: 1159
  helix: -0.62 (0.17), residues: 747
  sheet: -5.21 (0.67), residues: 11
  loop : -3.88 (0.26), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP H 430 
 HIS   0.007   0.001   HIS H 867 
 PHE   0.025   0.002   PHE H 270 
 TYR   0.020   0.002   TYR H1294 
 ARG   0.021   0.001   ARG H 598 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  264 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8723 (tp-100)
REVERT: H  268 VAL cc_start: 0.9007 (t) cc_final: 0.8349 (t)
REVERT: H  363 PHE cc_start: 0.7406 (t80) cc_final: 0.7156 (t80)
REVERT: H  367 LEU cc_start: 0.8871 (mt) cc_final: 0.8412 (mt)
REVERT: H  386 ASN cc_start: 0.6456 (m110) cc_final: 0.5461 (t0)
REVERT: H  445 ILE cc_start: 0.8957 (mt) cc_final: 0.8671 (pt)
REVERT: H  485 GLN cc_start: 0.8515 (pt0) cc_final: 0.8290 (pt0)
REVERT: H  580 LEU cc_start: 0.8516 (tp) cc_final: 0.8185 (tp)
REVERT: H  602 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7743 (mmtm)
REVERT: H 1200 LEU cc_start: 0.8461 (tt) cc_final: 0.8093 (tp)
REVERT: H 1280 LEU cc_start: 0.8548 (mt) cc_final: 0.8215 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1593
  time to fit residues: 36.3559
Evaluate side-chains
  102 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 444 GLN
H 474 GLN
H 817 HIS
H1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.079353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.062292 restraints weight = 33807.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.064275 restraints weight = 22579.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.065730 restraints weight = 16288.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.8295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7590  Z= 0.354
  Angle     :  0.886  12.854  10453  Z= 0.465
  Chirality :  0.051   0.359   1295
  Planarity :  0.007   0.089   1380
  Dihedral  :  5.749  41.169   1218
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.85 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  5.91 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.23), residues: 1159
  helix: -0.48 (0.18), residues: 743
  sheet: -4.52 (0.71), residues: 31
  loop : -3.43 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.005   TRP H 430 
 HIS   0.011   0.003   HIS H1098 
 PHE   0.048   0.004   PHE H1217 
 TYR   0.038   0.004   TYR H1254 
 ARG   0.015   0.002   ARG H 258 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  263 TYR cc_start: 0.8203 (t80) cc_final: 0.7827 (t80)
REVERT: H  304 THR cc_start: 0.9498 (m) cc_final: 0.9173 (p)
REVERT: H  400 MET cc_start: 0.8362 (ttm) cc_final: 0.7910 (ttt)
REVERT: H  418 CYS cc_start: 0.9303 (t) cc_final: 0.8829 (p)
REVERT: H  426 ASN cc_start: 0.9342 (p0) cc_final: 0.9114 (p0)
REVERT: H  445 ILE cc_start: 0.9445 (mt) cc_final: 0.9007 (mt)
REVERT: H  485 GLN cc_start: 0.8864 (pt0) cc_final: 0.8341 (pp30)
REVERT: H  559 PHE cc_start: 0.9068 (m-80) cc_final: 0.8854 (m-80)
REVERT: H  593 LEU cc_start: 0.9433 (tt) cc_final: 0.9180 (mm)
REVERT: H  609 LYS cc_start: 0.9648 (mmtm) cc_final: 0.9359 (mmmm)
REVERT: H 1183 ARG cc_start: 0.7278 (ttm170) cc_final: 0.6693 (tpp80)
REVERT: H 1202 SER cc_start: 0.8804 (m) cc_final: 0.8500 (t)
REVERT: H 1236 ILE cc_start: 0.9324 (tp) cc_final: 0.9088 (tp)
REVERT: H 1248 LEU cc_start: 0.9401 (tp) cc_final: 0.9092 (tp)
REVERT: H 1313 LYS cc_start: 0.8735 (tppt) cc_final: 0.8355 (pptt)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1546
  time to fit residues: 36.0088
Evaluate side-chains
  127 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 96 optimal weight:   30.0000
   chunk 81 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 64 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H1225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.079785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.062732 restraints weight = 32816.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064648 restraints weight = 22159.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.066056 restraints weight = 16157.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.8904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7590  Z= 0.160
  Angle     :  0.583   7.591  10453  Z= 0.305
  Chirality :  0.043   0.147   1295
  Planarity :  0.005   0.082   1380
  Dihedral  :  4.798  42.982   1218
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1159
  helix:  0.60 (0.19), residues: 738
  sheet: -4.38 (0.75), residues: 31
  loop : -3.26 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP H 430 
 HIS   0.006   0.001   HIS H 867 
 PHE   0.018   0.001   PHE H1177 
 TYR   0.030   0.001   TYR H1219 
 ARG   0.010   0.001   ARG H 598 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  233 MET cc_start: 0.7876 (mmp) cc_final: 0.7668 (mmm)
REVERT: H  260 LEU cc_start: 0.9097 (mm) cc_final: 0.8890 (tp)
REVERT: H  266 LEU cc_start: 0.9554 (tt) cc_final: 0.9059 (pp)
REVERT: H  267 CYS cc_start: 0.9207 (m) cc_final: 0.8893 (m)
REVERT: H  304 THR cc_start: 0.9335 (m) cc_final: 0.9107 (p)
REVERT: H  325 ASP cc_start: 0.7681 (m-30) cc_final: 0.7397 (m-30)
REVERT: H  363 PHE cc_start: 0.8094 (t80) cc_final: 0.7825 (t80)
REVERT: H  367 LEU cc_start: 0.9543 (mt) cc_final: 0.9311 (mt)
REVERT: H  385 ILE cc_start: 0.9140 (mt) cc_final: 0.8848 (tt)
REVERT: H  394 LYS cc_start: 0.9225 (tppp) cc_final: 0.8885 (tppt)
REVERT: H  396 TYR cc_start: 0.8603 (t80) cc_final: 0.8351 (t80)
REVERT: H  418 CYS cc_start: 0.9429 (t) cc_final: 0.9021 (p)
REVERT: H  444 GLN cc_start: 0.9286 (tp-100) cc_final: 0.9020 (tp-100)
REVERT: H  485 GLN cc_start: 0.8750 (pt0) cc_final: 0.8414 (pp30)
REVERT: H  543 SER cc_start: 0.9102 (m) cc_final: 0.8873 (p)
REVERT: H  546 MET cc_start: 0.7626 (mmp) cc_final: 0.7105 (mmp)
REVERT: H  559 PHE cc_start: 0.8951 (m-80) cc_final: 0.8684 (m-80)
REVERT: H  609 LYS cc_start: 0.9609 (mmtm) cc_final: 0.9272 (mmmm)
REVERT: H 1148 LEU cc_start: 0.9332 (mt) cc_final: 0.9132 (mt)
REVERT: H 1164 PHE cc_start: 0.8312 (t80) cc_final: 0.8049 (t80)
REVERT: H 1188 ASP cc_start: 0.8143 (t0) cc_final: 0.7777 (t0)
REVERT: H 1202 SER cc_start: 0.8788 (m) cc_final: 0.8452 (t)
REVERT: H 1203 HIS cc_start: 0.8678 (t70) cc_final: 0.8377 (t-90)
REVERT: H 1207 THR cc_start: 0.8136 (p) cc_final: 0.7688 (p)
REVERT: H 1223 PHE cc_start: 0.8362 (m-10) cc_final: 0.8141 (m-80)
REVERT: H 1225 GLN cc_start: 0.8539 (mp10) cc_final: 0.7933 (mp10)
REVERT: H 1246 ARG cc_start: 0.9157 (mmp80) cc_final: 0.8536 (mmp80)
REVERT: H 1302 LEU cc_start: 0.8760 (tp) cc_final: 0.8424 (tp)
REVERT: H 1306 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7608 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1569
  time to fit residues: 34.4070
Evaluate side-chains
  139 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0040
   chunk 18 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:   30.0000
   chunk 94 optimal weight:   30.0000
   overall best weight:    0.8794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.080193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.062895 restraints weight = 32866.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.064795 restraints weight = 22392.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.066248 restraints weight = 16502.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.9659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7590  Z= 0.157
  Angle     :  0.576   9.445  10453  Z= 0.299
  Chirality :  0.042   0.175   1295
  Planarity :  0.004   0.080   1380
  Dihedral  :  4.454  41.215   1218
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.25), residues: 1159
  helix:  0.97 (0.19), residues: 738
  sheet: -3.91 (0.73), residues: 38
  loop : -3.03 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP H 430 
 HIS   0.006   0.001   HIS H 867 
 PHE   0.018   0.001   PHE H1177 
 TYR   0.020   0.002   TYR H 263 
 ARG   0.004   0.001   ARG H 258 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  245 ILE cc_start: 0.9199 (tt) cc_final: 0.8931 (mp)
REVERT: H  266 LEU cc_start: 0.9545 (tt) cc_final: 0.9237 (pp)
REVERT: H  267 CYS cc_start: 0.9287 (m) cc_final: 0.8876 (m)
REVERT: H  304 THR cc_start: 0.9399 (m) cc_final: 0.9154 (p)
REVERT: H  325 ASP cc_start: 0.7260 (m-30) cc_final: 0.6972 (m-30)
REVERT: H  385 ILE cc_start: 0.9249 (mt) cc_final: 0.8878 (tt)
REVERT: H  396 TYR cc_start: 0.8349 (t80) cc_final: 0.7178 (t80)
REVERT: H  412 MET cc_start: 0.8370 (mpp) cc_final: 0.8159 (mpp)
REVERT: H  418 CYS cc_start: 0.9469 (t) cc_final: 0.9085 (p)
REVERT: H  441 MET cc_start: 0.9197 (tpp) cc_final: 0.8859 (tpp)
REVERT: H  543 SER cc_start: 0.9197 (m) cc_final: 0.8959 (p)
REVERT: H  559 PHE cc_start: 0.9008 (m-80) cc_final: 0.8622 (m-80)
REVERT: H  609 LYS cc_start: 0.9679 (mmtm) cc_final: 0.9345 (mmmm)
REVERT: H 1142 CYS cc_start: 0.8986 (m) cc_final: 0.8604 (t)
REVERT: H 1164 PHE cc_start: 0.8475 (t80) cc_final: 0.8205 (t80)
REVERT: H 1180 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8229 (tttt)
REVERT: H 1188 ASP cc_start: 0.8291 (t0) cc_final: 0.7856 (t0)
REVERT: H 1202 SER cc_start: 0.9049 (m) cc_final: 0.8646 (p)
REVERT: H 1246 ARG cc_start: 0.9057 (mmp80) cc_final: 0.8614 (mmp80)
REVERT: H 1302 LEU cc_start: 0.8838 (tp) cc_final: 0.8525 (tp)
REVERT: H 1304 ASP cc_start: 0.9090 (p0) cc_final: 0.8858 (p0)
REVERT: H 1306 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7580 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1399
  time to fit residues: 31.1153
Evaluate side-chains
  126 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0770
   chunk 53 optimal weight:   30.0000
   chunk 111 optimal weight:    2.9990
   chunk 113 optimal weight:   30.0000
   chunk 102 optimal weight:   30.0000
   chunk 100 optimal weight:   20.0000
   chunk 110 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    2.2146

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

Flipped N/Q/H residues before XYZ refinement:
** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 474 GLN
H1179 GLN
H1225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.074743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058671 restraints weight = 33037.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.060364 restraints weight = 22686.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.061651 restraints weight = 16797.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          1.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7590  Z= 0.265
  Angle     :  0.660   7.652  10453  Z= 0.350
  Chirality :  0.044   0.208   1295
  Planarity :  0.005   0.073   1380
  Dihedral  :  4.722  41.033   1218
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.38 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1159
  helix:  0.82 (0.20), residues: 735
  sheet: -4.46 (0.76), residues: 28
  loop : -2.93 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP H 232 
 HIS   0.006   0.001   HIS H 867 
 PHE   0.034   0.003   PHE H1177 
 TYR   0.020   0.003   TYR H1254 
 ARG   0.005   0.001   ARG H 388 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  292 CYS cc_start: 0.9216 (p) cc_final: 0.9006 (p)
REVERT: H  304 THR cc_start: 0.9645 (m) cc_final: 0.9397 (p)
REVERT: H  396 TYR cc_start: 0.8872 (t80) cc_final: 0.8579 (t80)
REVERT: H  418 CYS cc_start: 0.9624 (t) cc_final: 0.9244 (p)
REVERT: H  583 PHE cc_start: 0.9488 (m-10) cc_final: 0.8896 (m-80)
REVERT: H  598 ARG cc_start: 0.9341 (mmp80) cc_final: 0.9046 (mmp80)
REVERT: H  609 LYS cc_start: 0.9682 (mmtm) cc_final: 0.9340 (mmmm)
REVERT: H 1068 PHE cc_start: 0.8811 (t80) cc_final: 0.8610 (t80)
REVERT: H 1142 CYS cc_start: 0.9351 (m) cc_final: 0.9141 (t)
REVERT: H 1146 SER cc_start: 0.9560 (m) cc_final: 0.9231 (p)
REVERT: H 1188 ASP cc_start: 0.8968 (t0) cc_final: 0.8691 (t0)
REVERT: H 1202 SER cc_start: 0.9437 (m) cc_final: 0.9126 (p)
REVERT: H 1207 THR cc_start: 0.8757 (p) cc_final: 0.8289 (p)
REVERT: H 1223 PHE cc_start: 0.9108 (m-80) cc_final: 0.8767 (m-80)
REVERT: H 1233 SER cc_start: 0.9812 (m) cc_final: 0.9451 (p)
REVERT: H 1246 ARG cc_start: 0.9008 (mmp80) cc_final: 0.8706 (mmp80)
REVERT: H 1290 MET cc_start: 0.9143 (mmp) cc_final: 0.8770 (mmm)
REVERT: H 1302 LEU cc_start: 0.9041 (tp) cc_final: 0.8282 (tp)
REVERT: H 1304 ASP cc_start: 0.9204 (p0) cc_final: 0.8893 (p0)
REVERT: H 1306 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7914 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1424
  time to fit residues: 32.8129
Evaluate side-chains
  130 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 115 optimal weight:   20.0000
   chunk 56 optimal weight:   20.0000
   chunk 48 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 59 optimal weight:   20.0000
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** H 392 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 = 0.3459 r_free = 0.3459 target = 0.077644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.060561 restraints weight = 33358.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.062395 restraints weight = 22480.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.063775 restraints weight = 16433.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          1.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7590  Z= 0.189
  Angle     :  0.598   6.823  10453  Z= 0.313
  Chirality :  0.043   0.192   1295
  Planarity :  0.004   0.077   1380
  Dihedral  :  4.417  37.840   1218
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.25), residues: 1159
  helix:  1.20 (0.20), residues: 737
  sheet: -4.34 (0.79), residues: 29
  loop : -2.94 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP H 232 
 HIS   0.006   0.001   HIS H 867 
 PHE   0.020   0.002   PHE H1164 
 TYR   0.018   0.002   TYR H 263 
 ARG   0.004   0.001   ARG H 388 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  264 GLN cc_start: 0.8939 (mp10) cc_final: 0.8705 (mp10)
REVERT: H  292 CYS cc_start: 0.9146 (p) cc_final: 0.8945 (p)
REVERT: H  304 THR cc_start: 0.9618 (m) cc_final: 0.9378 (p)
REVERT: H  308 LEU cc_start: 0.9305 (mm) cc_final: 0.8986 (pp)
REVERT: H  325 ASP cc_start: 0.7965 (m-30) cc_final: 0.7504 (m-30)
REVERT: H  400 MET cc_start: 0.8619 (ttm) cc_final: 0.8290 (tpp)
REVERT: H  418 CYS cc_start: 0.9601 (t) cc_final: 0.9249 (p)
REVERT: H  580 LEU cc_start: 0.9524 (tp) cc_final: 0.9308 (tp)
REVERT: H  583 PHE cc_start: 0.9401 (m-10) cc_final: 0.8826 (m-80)
REVERT: H  598 ARG cc_start: 0.9352 (mmp80) cc_final: 0.9020 (mmp80)
REVERT: H  609 LYS cc_start: 0.9684 (mmtm) cc_final: 0.9329 (mmmm)
REVERT: H 1142 CYS cc_start: 0.9382 (m) cc_final: 0.9179 (t)
REVERT: H 1146 SER cc_start: 0.9620 (m) cc_final: 0.9266 (p)
REVERT: H 1147 THR cc_start: 0.9468 (t) cc_final: 0.9220 (p)
REVERT: H 1179 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8413 (tp40)
REVERT: H 1180 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8722 (tttt)
REVERT: H 1188 ASP cc_start: 0.8946 (t0) cc_final: 0.8527 (t0)
REVERT: H 1207 THR cc_start: 0.8560 (p) cc_final: 0.7981 (p)
REVERT: H 1233 SER cc_start: 0.9772 (m) cc_final: 0.9418 (p)
REVERT: H 1246 ARG cc_start: 0.9064 (mmp80) cc_final: 0.8503 (mmp80)
REVERT: H 1302 LEU cc_start: 0.9050 (tp) cc_final: 0.8279 (tp)
REVERT: H 1304 ASP cc_start: 0.9120 (p0) cc_final: 0.8662 (p0)
REVERT: H 1306 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7859 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1511
  time to fit residues: 35.2601
Evaluate side-chains
  141 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    0.1980
   chunk 90 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 115 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
H 392 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.072353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.056078 restraints weight = 34395.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057758 restraints weight = 23285.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.059044 restraints weight = 17119.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          1.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7590  Z= 0.311
  Angle     :  0.712   8.985  10453  Z= 0.381
  Chirality :  0.045   0.210   1295
  Planarity :  0.005   0.071   1380
  Dihedral  :  4.802  38.927   1218
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.25), residues: 1159
  helix:  0.79 (0.20), residues: 742
  sheet: -4.57 (0.69), residues: 29
  loop : -2.86 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP H 232 
 HIS   0.007   0.002   HIS H1203 
 PHE   0.022   0.002   PHE H 431 
 TYR   0.030   0.003   TYR H1254 
 ARG   0.005   0.001   ARG H1222 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  396 TYR cc_start: 0.8983 (t80) cc_final: 0.8654 (t80)
REVERT: H  398 LYS cc_start: 0.9760 (tptp) cc_final: 0.9342 (tptt)
REVERT: H  400 MET cc_start: 0.8744 (ttm) cc_final: 0.8423 (tpp)
REVERT: H  418 CYS cc_start: 0.9734 (t) cc_final: 0.9425 (p)
REVERT: H  598 ARG cc_start: 0.9242 (mmp80) cc_final: 0.8882 (mmp80)
REVERT: H  609 LYS cc_start: 0.9689 (mmtm) cc_final: 0.9236 (mmmm)
REVERT: H  612 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8780 (mt-10)
REVERT: H 1146 SER cc_start: 0.9758 (m) cc_final: 0.9494 (p)
REVERT: H 1179 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8671 (tp40)
REVERT: H 1188 ASP cc_start: 0.9143 (t0) cc_final: 0.8739 (t0)
REVERT: H 1229 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8478 (mt-10)
REVERT: H 1233 SER cc_start: 0.9768 (m) cc_final: 0.9427 (p)
REVERT: H 1246 ARG cc_start: 0.8986 (mmp80) cc_final: 0.8723 (mmp80)
REVERT: H 1249 GLU cc_start: 0.9067 (pp20) cc_final: 0.8526 (pp20)
REVERT: H 1290 MET cc_start: 0.9088 (mmp) cc_final: 0.8684 (mmm)
REVERT: H 1302 LEU cc_start: 0.9398 (tp) cc_final: 0.8950 (tp)
REVERT: H 1306 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8582 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1396
  time to fit residues: 34.4752
Evaluate side-chains
  142 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.077095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.060101 restraints weight = 33917.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.061928 restraints weight = 22864.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.063139 restraints weight = 16716.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          1.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7590  Z= 0.161
  Angle     :  0.585   6.898  10453  Z= 0.305
  Chirality :  0.043   0.162   1295
  Planarity :  0.004   0.073   1380
  Dihedral  :  4.354  35.750   1218
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.09 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.26), residues: 1159
  helix:  1.30 (0.20), residues: 744
  sheet: -3.82 (0.72), residues: 38
  loop : -2.82 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP H 232 
 HIS   0.005   0.001   HIS H 867 
 PHE   0.028   0.002   PHE H1164 
 TYR   0.022   0.001   TYR H1181 
 ARG   0.004   0.001   ARG H 598 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  264 GLN cc_start: 0.8978 (mp10) cc_final: 0.8709 (mp10)
REVERT: H  325 ASP cc_start: 0.8200 (m-30) cc_final: 0.7838 (m-30)
REVERT: H  396 TYR cc_start: 0.8903 (t80) cc_final: 0.8499 (t80)
REVERT: H  398 LYS cc_start: 0.9716 (tptp) cc_final: 0.9425 (tptt)
REVERT: H  418 CYS cc_start: 0.9710 (t) cc_final: 0.9124 (p)
REVERT: H  590 LEU cc_start: 0.9678 (mp) cc_final: 0.9293 (tt)
REVERT: H  598 ARG cc_start: 0.9202 (mmp80) cc_final: 0.8831 (mmp80)
REVERT: H  609 LYS cc_start: 0.9684 (mmtm) cc_final: 0.9333 (mmmm)
REVERT: H 1140 LEU cc_start: 0.9731 (tt) cc_final: 0.9426 (pp)
REVERT: H 1146 SER cc_start: 0.9721 (m) cc_final: 0.9471 (p)
REVERT: H 1175 CYS cc_start: 0.9215 (m) cc_final: 0.8965 (m)
REVERT: H 1180 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8693 (tttt)
REVERT: H 1188 ASP cc_start: 0.8986 (t0) cc_final: 0.8597 (t0)
REVERT: H 1206 GLU cc_start: 0.8927 (tt0) cc_final: 0.8290 (tp30)
REVERT: H 1229 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8506 (mt-10)
REVERT: H 1233 SER cc_start: 0.9748 (m) cc_final: 0.9421 (p)
REVERT: H 1234 ASN cc_start: 0.9494 (t0) cc_final: 0.9124 (t0)
REVERT: H 1246 ARG cc_start: 0.9080 (mmp80) cc_final: 0.8477 (mmp80)
REVERT: H 1255 ILE cc_start: 0.8978 (mm) cc_final: 0.8751 (mm)
REVERT: H 1290 MET cc_start: 0.8963 (mmp) cc_final: 0.8544 (mmm)
REVERT: H 1302 LEU cc_start: 0.9118 (tp) cc_final: 0.8468 (tp)
REVERT: H 1306 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8425 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1517
  time to fit residues: 38.1658
Evaluate side-chains
  147 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0570
   chunk 81 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 113 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.9900

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

Flipped N/Q/H residues before XYZ refinement:
** H1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H1225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.076872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059829 restraints weight = 34237.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.061659 restraints weight = 23086.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.063011 restraints weight = 16941.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          1.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7590  Z= 0.171
  Angle     :  0.600   7.850  10453  Z= 0.310
  Chirality :  0.043   0.178   1295
  Planarity :  0.004   0.070   1380
  Dihedral  :  4.196  37.369   1218
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1159
  helix:  1.47 (0.20), residues: 746
  sheet: -3.89 (0.87), residues: 27
  loop : -2.77 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP H 232 
 HIS   0.005   0.001   HIS H 867 
 PHE   0.017   0.002   PHE H1177 
 TYR   0.019   0.001   TYR H1181 
 ARG   0.003   0.000   ARG H 598 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  271 ASP cc_start: 0.8865 (m-30) cc_final: 0.8624 (m-30)
REVERT: H  292 CYS cc_start: 0.9260 (t) cc_final: 0.8272 (p)
REVERT: H  325 ASP cc_start: 0.8085 (m-30) cc_final: 0.7640 (m-30)
REVERT: H  385 ILE cc_start: 0.9504 (mt) cc_final: 0.9228 (tp)
REVERT: H  396 TYR cc_start: 0.8916 (t80) cc_final: 0.8491 (t80)
REVERT: H  398 LYS cc_start: 0.9722 (tptp) cc_final: 0.9447 (tptt)
REVERT: H  400 MET cc_start: 0.9014 (ttm) cc_final: 0.8514 (ttm)
REVERT: H  418 CYS cc_start: 0.9699 (t) cc_final: 0.9094 (p)
REVERT: H  429 MET cc_start: 0.7846 (mtt) cc_final: 0.7374 (mmm)
REVERT: H  590 LEU cc_start: 0.9699 (mp) cc_final: 0.9400 (tt)
REVERT: H  598 ARG cc_start: 0.9211 (mmp80) cc_final: 0.8816 (mmp80)
REVERT: H 1140 LEU cc_start: 0.9804 (tt) cc_final: 0.9495 (pp)
REVERT: H 1146 SER cc_start: 0.9687 (m) cc_final: 0.9456 (p)
REVERT: H 1156 VAL cc_start: 0.9829 (p) cc_final: 0.9597 (m)
REVERT: H 1180 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8598 (tttt)
REVERT: H 1188 ASP cc_start: 0.8912 (t0) cc_final: 0.8460 (t0)
REVERT: H 1206 GLU cc_start: 0.9054 (tt0) cc_final: 0.8311 (tp30)
REVERT: H 1229 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8511 (mt-10)
REVERT: H 1233 SER cc_start: 0.9789 (m) cc_final: 0.9455 (p)
REVERT: H 1246 ARG cc_start: 0.8872 (mmp80) cc_final: 0.8301 (mmp80)
REVERT: H 1249 GLU cc_start: 0.9069 (pp20) cc_final: 0.8760 (pp20)
REVERT: H 1290 MET cc_start: 0.8956 (mmp) cc_final: 0.8367 (mmm)
REVERT: H 1293 ASN cc_start: 0.9253 (p0) cc_final: 0.8793 (t0)
REVERT: H 1302 LEU cc_start: 0.9222 (tp) cc_final: 0.8426 (tp)
REVERT: H 1306 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8546 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1406
  time to fit residues: 34.5516
Evaluate side-chains
  145 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 94 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 115 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 59 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0020
   chunk 39 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.9994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.075004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057885 restraints weight = 34323.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.059610 restraints weight = 23275.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.060743 restraints weight = 17168.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          1.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7590  Z= 0.223
  Angle     :  0.629   8.117  10453  Z= 0.327
  Chirality :  0.045   0.194   1295
  Planarity :  0.004   0.066   1380
  Dihedral  :  4.324  34.846   1218
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.04 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1159
  helix:  1.45 (0.20), residues: 739
  sheet: -4.29 (0.75), residues: 29
  loop : -2.70 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP H 232 
 HIS   0.005   0.001   HIS H 867 
 PHE   0.017   0.002   PHE H1164 
 TYR   0.025   0.002   TYR H1287 
 ARG   0.002   0.000   ARG H 258 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2164.36 seconds
wall clock time: 38 minutes 10.57 seconds (2290.57 seconds total)