Starting phenix.real_space_refine
on Fri Dec  8 06:56:18 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_20534_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_20534.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_20534.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_20534_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/12_2023/6pzc_20534_neut.pdb"
  }
  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
    Residue "H ARG  289": "NH1" <-> "NH2"
    Residue "H ARG  298": "NH1" <-> "NH2"
    Residue "H ARG  306": "NH1" <-> "NH2"
    Residue "H ARG  598": "NH1" <-> "NH2"
    Residue "H ARG  702": "NH1" <-> "NH2"
    Residue "H ARG 1300": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.71, per 1000 atoms: 0.63
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.6 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: 0.97
  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: 2.58

  Time building geometry restraints manager: 3.49 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:
       97.32 -   104.65: 106
      104.65 -   111.98: 3809
      111.98 -   119.32: 2439
      119.32 -   126.65: 4004
      126.65 -   133.99: 95
  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 2.520
  nonbonded pdb=" N   ASN H 781 "
            pdb=" OE2 GLU H1206 "
     model   vdw
     2.154 2.520
  nonbonded pdb=" O   LEU H1192 "
            pdb=" OG1 THR H1196 "
     model   vdw
     2.211 2.440
  nonbonded pdb=" O   LEU H 367 "
            pdb=" OG1 THR H 371 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" O   LEU H1148 "
            pdb=" OG  SER H1152 "
     model   vdw
     2.247 2.440
  ... (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:             0.210
  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:          1.250
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     25.050
  Find NCS groups from input model:        0.250
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.960
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2080
  time to fit residues: 44.4127
Evaluate side-chains
  105 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.775 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1411
-------------------------------------------------------------------------------
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:   20.0000
   chunk 88 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 386 ASN
H1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.5656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.097   7590  Z= 0.370
  Angle     :  0.814  10.517  10453  Z= 0.442
  Chirality :  0.047   0.221   1295
  Planarity :  0.007   0.096   1380
  Dihedral  :  6.097  44.825   1218
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  4.22 %
    Favored  : 94.94 %
  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: -2.73 (0.23), residues: 1159
  helix: -0.69 (0.18), residues: 750
  sheet: -4.95 (0.58), residues: 21
  loop : -3.86 (0.27), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.076   0.006   TRP H 430 
   HIS   0.009   0.002   HIS H 867 
   PHE   0.036   0.003   PHE H 270 
   TYR   0.028   0.004   TYR H1254 
   ARG   0.017   0.002   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
  169 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 165
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 169
  average time/residue: 0.1611
  time to fit residues: 38.6778
Evaluate side-chains
  126 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.840 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0649
  time to fit residues: 1.1162
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 106 optimal weight:    0.2980
   chunk 114 optimal weight:    0.6980
   chunk 94 optimal weight:   30.0000
   chunk 105 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
H 392 GLN
H 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.6605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7590  Z= 0.173
  Angle     :  0.597   8.053  10453  Z= 0.316
  Chirality :  0.043   0.159   1295
  Planarity :  0.005   0.092   1380
  Dihedral  :  5.287  44.095   1218
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  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: -1.57 (0.24), residues: 1159
  helix:  0.37 (0.19), residues: 745
  sheet: -4.48 (0.72), residues: 21
  loop : -3.73 (0.26), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.002   TRP H 430 
   HIS   0.008   0.001   HIS H 867 
   PHE   0.022   0.002   PHE H 314 
   TYR   0.039   0.002   TYR H1219 
   ARG   0.008   0.001   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
  153 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1568
  time to fit residues: 34.3999
Evaluate side-chains
  122 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.885 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0928
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
H 241 HIS
H 817 HIS
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H1301 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          1.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082   7590  Z= 0.520
  Angle     :  1.072  16.125  10453  Z= 0.564
  Chirality :  0.051   0.245   1295
  Planarity :  0.008   0.081   1380
  Dihedral  :  6.727  40.388   1218
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 22.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.65 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.70 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.23), residues: 1159
  helix: -0.51 (0.18), residues: 728
  sheet: -4.76 (0.57), residues: 31
  loop : -3.59 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.106   0.005   TRP H 430 
   HIS   0.012   0.004   HIS H 562 
   PHE   0.040   0.004   PHE H 295 
   TYR   0.057   0.004   TYR H1254 
   ARG   0.017   0.002   ARG H1218 

*********************** 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
  181 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 175
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1515
  time to fit residues: 38.9461
Evaluate side-chains
  134 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.826 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0710
  time to fit residues: 1.2129
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 96 optimal weight:   20.0000
   chunk 78 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H1225 GLN
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          1.2897

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= 0.179
  Angle     :  0.624   7.253  10453  Z= 0.332
  Chirality :  0.043   0.187   1295
  Planarity :  0.005   0.083   1380
  Dihedral  :  5.381  39.790   1218
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.74 %
    Favored  : 97.05 %
  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: -1.30 (0.25), residues: 1159
  helix:  0.57 (0.19), residues: 728
  sheet: -4.67 (0.63), residues: 21
  loop : -3.42 (0.27), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.057   0.003   TRP H 430 
   HIS   0.008   0.001   HIS H 867 
   PHE   0.025   0.002   PHE H1177 
   TYR   0.023   0.002   TYR H1219 
   ARG   0.004   0.000   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
  180 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 180
  average time/residue: 0.1404
  time to fit residues: 37.6938
Evaluate side-chains
  141 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.891 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0706
  time to fit residues: 1.2535
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    0.4980
   chunk 22 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 113 optimal weight:   30.0000
   chunk 93 optimal weight:    0.4980
   chunk 52 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:   20.0000
   chunk 109 optimal weight:   20.0000
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
H 386 ASN
H1225 GLN
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H1293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          1.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7590  Z= 0.263
  Angle     :  0.676   8.819  10453  Z= 0.362
  Chirality :  0.044   0.175   1295
  Planarity :  0.005   0.076   1380
  Dihedral  :  5.218  40.024   1218
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  3.38 %
    Favored  : 96.20 %
  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: -1.10 (0.25), residues: 1159
  helix:  0.68 (0.19), residues: 735
  sheet: -4.65 (0.61), residues: 31
  loop : -3.23 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.031   0.002   TRP H 232 
   HIS   0.006   0.002   HIS H 867 
   PHE   0.021   0.002   PHE H 431 
   TYR   0.023   0.002   TYR H 263 
   ARG   0.006   0.001   ARG H1246 

*********************** 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
  163 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 163
  average time/residue: 0.1513
  time to fit residues: 35.4430
Evaluate side-chains
  139 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.845 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0689
  time to fit residues: 1.2277
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 95 optimal weight:   20.0000
   chunk 63 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H1203 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          1.3970

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= 0.175
  Angle     :  0.590   9.593  10453  Z= 0.305
  Chirality :  0.042   0.157   1295
  Planarity :  0.005   0.078   1380
  Dihedral  :  4.650  37.878   1218
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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: -0.47 (0.26), residues: 1159
  helix:  1.22 (0.20), residues: 735
  sheet: -4.61 (0.61), residues: 31
  loop : -3.06 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP H1247 
   HIS   0.007   0.001   HIS H 867 
   PHE   0.018   0.001   PHE H1164 
   TYR   0.017   0.002   TYR H 263 
   ARG   0.008   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
  169 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1504
  time to fit residues: 36.8958
Evaluate side-chains
  139 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.881 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1570
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0270
   chunk 102 optimal weight:    9.9990
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
H 262 ASN
H 386 ASN
H 397 ASN
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          1.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063   7590  Z= 0.161
  Angle     :  0.592   9.184  10453  Z= 0.299
  Chirality :  0.042   0.154   1295
  Planarity :  0.004   0.073   1380
  Dihedral  :  4.479  38.759   1218
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.52 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  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: -0.21 (0.26), residues: 1159
  helix:  1.42 (0.20), residues: 735
  sheet: -4.48 (0.65), residues: 31
  loop : -2.95 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP H1247 
   HIS   0.007   0.001   HIS H 867 
   PHE   0.015   0.002   PHE H1177 
   TYR   0.018   0.002   TYR H 377 
   ARG   0.008   0.001   ARG H1145 

*********************** 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
  169 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1434
  time to fit residues: 35.9957
Evaluate side-chains
  142 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1339
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 108 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 99 optimal weight:    9.9990
   chunk 104 optimal weight:    0.0020
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
H 397 ASN
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          1.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7590  Z= 0.190
  Angle     :  0.608   6.785  10453  Z= 0.313
  Chirality :  0.042   0.158   1295
  Planarity :  0.004   0.071   1380
  Dihedral  :  4.367  36.906   1218
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  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: -0.02 (0.26), residues: 1159
  helix:  1.57 (0.20), residues: 734
  sheet: -3.93 (0.69), residues: 38
  loop : -2.87 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP H 232 
   HIS   0.006   0.001   HIS H 867 
   PHE   0.024   0.002   PHE H 432 
   TYR   0.028   0.002   TYR H1294 
   ARG   0.006   0.001   ARG H1145 

*********************** 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
  162 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1407
  time to fit residues: 34.1376
Evaluate side-chains
  137 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.841 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1389
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 116 optimal weight:    6.9990
   chunk 107 optimal weight:    0.0070
   chunk 92 optimal weight:   40.0000
   chunk 9 optimal weight:    0.0010
   chunk 71 optimal weight:    0.1980
   chunk 56 optimal weight:   20.0000
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.3804

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

Flipped N/Q/H residues before XYZ refinement:
H 234 ASN
H 386 ASN
H 397 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          1.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7590  Z= 0.156
  Angle     :  0.605   7.967  10453  Z= 0.301
  Chirality :  0.042   0.154   1295
  Planarity :  0.004   0.071   1380
  Dihedral  :  4.145  36.589   1218
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.75 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  0.21 (0.26), residues: 1159
  helix:  1.71 (0.20), residues: 741
  sheet: -3.49 (0.75), residues: 36
  loop : -2.84 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP H1247 
   HIS   0.006   0.001   HIS H 867 
   PHE   0.020   0.001   PHE H1223 
   TYR   0.019   0.001   TYR H 396 
   ARG   0.007   0.001   ARG H1145 

********************** 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
  169 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1422
  time to fit residues: 35.5982
Evaluate side-chains
  139 residues out of total 1015 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1401
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 92 optimal weight:    0.3980
   chunk 38 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 397 ASN
** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H1293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.073005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.056010 restraints weight = 35110.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.057641 restraints weight = 23884.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.058889 restraints weight = 17668.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          1.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7590  Z= 0.256
  Angle     :  0.658   7.960  10453  Z= 0.341
  Chirality :  0.044   0.166   1295
  Planarity :  0.005   0.065   1380
  Dihedral  :  4.360  35.705   1218
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.95 %
    Favored  : 93.96 %
  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:  0.10 (0.26), residues: 1159
  helix:  1.60 (0.20), residues: 736
  sheet: -3.65 (0.70), residues: 38
  loop : -2.70 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.002   TRP H 232 
   HIS   0.006   0.001   HIS H 867 
   PHE   0.021   0.002   PHE H1164 
   TYR   0.029   0.002   TYR H1181 
   ARG   0.006   0.001   ARG H1246 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1539.42 seconds
wall clock time: 28 minutes 35.75 seconds (1715.75 seconds total)