Starting phenix.real_space_refine
on Wed Nov 15 14:48:46 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/11_2023/8fdg_29011.pdb"
  }
  resolution = 3.2
  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=   1.000
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      55      5.16       5
     C    7707      2.51       5
     N    2064      2.21       5
     O    2337      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 12163
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1505, 12163
          Classifications: {'peptide': 1505}
          Link IDs: {'PTRANS': 76, 'TRANS': 1428}
  Time building chain proxies: 6.27, per 1000 atoms: 0.52
  Number of scatterers: 12163
  At special positions: 0
  Unit cell: (92.7, 110.7, 142.2, 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      55     16.00
     O    2337      8.00
     N    2064      7.00
     C    7707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 139 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 472 " - pdb=" SG  CYS A 498 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 575 " - pdb=" SG  CYS A 656 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 994 " - pdb=" SG  CYS A1020 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1176 " - pdb=" SG  CYS A1330 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1335 " - pdb=" SG  CYS A1490 " distance=2.04

  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: 4.17
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2838

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 21 sheets defined
      5.1% alpha, 28.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 149 through 155
      removed outlier: 3.686A  pdb=" N   PHE A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASN A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 290
      removed outlier: 3.786A  pdb=" N   ALA A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 464
      removed outlier: 3.667A  pdb=" N   GLU A 464 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 489
      removed outlier: 3.516A  pdb=" N   SER A 489 " --> pdb=" O   ARG A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 539
      removed outlier: 3.545A  pdb=" N   ASN A 534 " --> pdb=" O   TYR A 530 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   CYS A 539 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 760 through 764
      removed outlier: 4.281A  pdb=" N   SER A 764 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 986
    Processing helix  chain 'A' and resid 1057 through 1062
    Processing helix  chain 'A' and resid 1188 through 1190
      No H-bonds generated for 'chain 'A' and resid 1188 through 1190'
    Processing helix  chain 'A' and resid 1203 through 1207
      removed outlier: 3.877A  pdb=" N   ALA A1206 " --> pdb=" O   PRO A1203 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ARG A1207 " --> pdb=" O   ARG A1204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1203 through 1207'
    Processing helix  chain 'A' and resid 1501 through 1505
      removed outlier: 3.889A  pdb=" N   LYS A1505 " --> pdb=" O   ILE A1502 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 6.163A  pdb=" N   ARG A   4 " --> pdb=" O   LYS A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 40
      removed outlier: 3.759A  pdb=" N   LYS A  75 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A  10 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 65
    Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 185
      removed outlier: 3.725A  pdb=" N   LYS A 181 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN A 269 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU A 249 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191
    Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219
      removed outlier: 6.178A  pdb=" N   ILE A 217 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY A 276 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 370
      removed outlier: 3.650A  pdb=" N   LYS A 408 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 328 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET A 410 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASP A 401 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 395 through 397
      removed outlier: 6.696A  pdb=" N   ILE A 395 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   CYS A 498 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ALA A 397 " --> pdb=" O   CYS A 498 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR A 478 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 515
      removed outlier: 7.221A  pdb=" N   THR A 579 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   ASP A 513 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLN A 581 " --> pdb=" O   ASP A 513 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU A 515 " --> pdb=" O   GLN A 581 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS A 583 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE A 520 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 511 through 515
      removed outlier: 7.221A  pdb=" N   THR A 579 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   ASP A 513 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLN A 581 " --> pdb=" O   ASP A 513 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU A 515 " --> pdb=" O   GLN A 581 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS A 583 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 575
      removed outlier: 6.675A  pdb=" N   LEU A 572 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   VAL A 654 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   PHE A 574 " --> pdb=" O   VAL A 654 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 594 through 596
      removed outlier: 3.680A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 883 through 891
      removed outlier: 6.194A  pdb=" N   ARG A 849 " --> pdb=" O   GLN A 926 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG A 928 " --> pdb=" O   ARG A 849 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TYR A 851 " --> pdb=" O   ARG A 928 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   LYS A 930 " --> pdb=" O   TYR A 851 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE A 853 " --> pdb=" O   LYS A 930 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A 973 " --> pdb=" O   ASN A 931 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 917 through 920
      removed outlier: 6.322A  pdb=" N   ILE A 917 " --> pdb=" O   LEU A1018 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   CYS A1020 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA A 919 " --> pdb=" O   CYS A1020 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A1019 " --> pdb=" O   ARG A 995 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG A 995 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1036 through 1041
      removed outlier: 4.456A  pdb=" N   ARG A1036 " --> pdb=" O   TRP A1094 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089
      removed outlier: 3.750A  pdb=" N   MET A1089 " --> pdb=" O   LEU A1170 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN A1154 " --> pdb=" O   HIS A1112 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TRP A1131 " --> pdb=" O   VAL A1111 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1120
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1178 through 1179
      removed outlier: 3.677A  pdb=" N   MET A1178 " --> pdb=" O   GLY A1329 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLU A1326 " --> pdb=" O   ILE A1245 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ILE A1245 " --> pdb=" O   GLU A1326 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLN A1328 " --> pdb=" O   THR A1243 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   GLN A1233 " --> pdb=" O   ARG A1311 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ARG A1311 " --> pdb=" O   GLN A1233 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASP A1235 " --> pdb=" O   TYR A1309 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   TYR A1309 " --> pdb=" O   ASP A1235 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A1237 " --> pdb=" O   ALA A1307 " (cutoff:3.500A)
      removed outlier: 10.807A  pdb=" N   ALA A1307 " --> pdb=" O   GLN A1237 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLU A1239 " --> pdb=" O   ILE A1305 " (cutoff:3.500A)
      removed outlier: 10.934A  pdb=" N   ILE A1305 " --> pdb=" O   GLU A1239 " (cutoff:3.500A)
      removed outlier: 10.112A  pdb=" N   ILE A1241 " --> pdb=" O   PRO A1303 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   THR A1243 " --> pdb=" O   PHE A1301 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A1245 " --> pdb=" O   ASN A1299 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE A1310 " --> pdb=" O   TYR A1266 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   TYR A1266 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE A1312 " --> pdb=" O   VAL A1264 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL A1264 " --> pdb=" O   ILE A1312 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   PHE A1262 " --> pdb=" O   PRO A1314 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ARG A1316 " --> pdb=" O   THR A1260 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1192 through 1193
      removed outlier: 7.022A  pdb=" N   GLN A1233 " --> pdb=" O   ARG A1311 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ARG A1311 " --> pdb=" O   GLN A1233 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASP A1235 " --> pdb=" O   TYR A1309 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   TYR A1309 " --> pdb=" O   ASP A1235 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A1237 " --> pdb=" O   ALA A1307 " (cutoff:3.500A)
      removed outlier: 10.807A  pdb=" N   ALA A1307 " --> pdb=" O   GLN A1237 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLU A1239 " --> pdb=" O   ILE A1305 " (cutoff:3.500A)
      removed outlier: 10.934A  pdb=" N   ILE A1305 " --> pdb=" O   GLU A1239 " (cutoff:3.500A)
      removed outlier: 10.112A  pdb=" N   ILE A1241 " --> pdb=" O   PRO A1303 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   THR A1243 " --> pdb=" O   PHE A1301 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A1245 " --> pdb=" O   ASN A1299 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE A1310 " --> pdb=" O   TYR A1266 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   TYR A1266 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE A1312 " --> pdb=" O   VAL A1264 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL A1264 " --> pdb=" O   ILE A1312 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   PHE A1262 " --> pdb=" O   PRO A1314 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ARG A1316 " --> pdb=" O   THR A1260 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A1266 " --> pdb=" O   GLN A1274 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1217 through 1218
      removed outlier: 3.820A  pdb=" N   TRP A1217 " --> pdb=" O   LEU A1323 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A1323 " --> pdb=" O   TRP A1217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1434 through 1435
      removed outlier: 3.730A  pdb=" N   TYR A1426 " --> pdb=" O   LYS A1434 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL A1419 " --> pdb=" O   TRP A1477 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP A1477 " --> pdb=" O   VAL A1419 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   SER A1421 " --> pdb=" O   LYS A1475 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A1427 " --> pdb=" O   PHE A1469 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE A1469 " --> pdb=" O   SER A1427 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A1461 " --> pdb=" O   THR A1403 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   THR A1403 " --> pdb=" O   PHE A1461 " (cutoff:3.500A)
      removed outlier: 10.037A  pdb=" N   LYS A1401 " --> pdb=" O   PRO A1463 " (cutoff:3.500A)
      removed outlier: 10.790A  pdb=" N   ILE A1465 " --> pdb=" O   ILE A1399 " (cutoff:3.500A)
      removed outlier: 9.369A  pdb=" N   ILE A1399 " --> pdb=" O   ILE A1465 " (cutoff:3.500A)
      removed outlier: 9.690A  pdb=" N   SER A1467 " --> pdb=" O   LEU A1397 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   LEU A1397 " --> pdb=" O   SER A1467 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   PHE A1469 " --> pdb=" O   ASP A1395 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ASP A1395 " --> pdb=" O   PHE A1469 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ARG A1471 " --> pdb=" O   GLU A1393 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLU A1393 " --> pdb=" O   ARG A1471 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   PHE A1488 " --> pdb=" O   THR A1403 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ILE A1405 " --> pdb=" O   GLU A1486 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLU A1486 " --> pdb=" O   ILE A1405 " (cutoff:3.500A)

    193 hydrogen bonds defined for protein.
    483 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: 5.04

  Time building geometry restraints manager: 4.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3967
        1.34 -     1.47: 3113
        1.47 -     1.60: 5305
        1.60 -     1.72: 0
        1.72 -     1.85: 92
  Bond restraints: 12477
  Sorted by residual:
  bond pdb=" C   ILE A 339 "
       pdb=" N   PRO A 340 "
    ideal  model  delta    sigma   weight residual
    1.330  1.364 -0.034 1.22e-02 6.72e+03 7.96e+00
  bond pdb=" CA  GLU A 907 "
       pdb=" CB  GLU A 907 "
    ideal  model  delta    sigma   weight residual
    1.526  1.562 -0.035 1.76e-02 3.23e+03 4.05e+00
  bond pdb=" N   GLU A1494 "
       pdb=" CA  GLU A1494 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.10e-02 8.26e+03 3.17e+00
  bond pdb=" CB  CYS A 498 "
       pdb=" SG  CYS A 498 "
    ideal  model  delta    sigma   weight residual
    1.808  1.848 -0.040 3.30e-02 9.18e+02 1.47e+00
  bond pdb=" C   PRO A 670 "
       pdb=" N   PRO A 671 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.027 2.34e-02 1.83e+03 1.29e+00
  ... (remaining 12472 not shown)

  Histogram of bond angle deviations from ideal:
      100.03 -   106.83: 412
      106.83 -   113.64: 6666
      113.64 -   120.44: 4498
      120.44 -   127.24: 5171
      127.24 -   134.04: 167
  Bond angle restraints: 16914
  Sorted by residual:
  angle pdb=" C   ARG A1282 "
        pdb=" N   ASN A1283 "
        pdb=" CA  ASN A1283 "
      ideal   model   delta    sigma   weight residual
     121.54  132.50  -10.96 1.91e+00 2.74e-01 3.29e+01
  angle pdb=" N   VAL A1033 "
        pdb=" CA  VAL A1033 "
        pdb=" C   VAL A1033 "
      ideal   model   delta    sigma   weight residual
     113.53  110.14    3.39 9.80e-01 1.04e+00 1.20e+01
  angle pdb=" CA  ILE A 878 "
        pdb=" C   ILE A 878 "
        pdb=" N   PRO A 879 "
      ideal   model   delta    sigma   weight residual
     116.57  119.65   -3.08 9.80e-01 1.04e+00 9.85e+00
  angle pdb=" C   VAL A1332 "
        pdb=" N   ASN A1333 "
        pdb=" CA  ASN A1333 "
      ideal   model   delta    sigma   weight residual
     121.54  127.50   -5.96 1.91e+00 2.74e-01 9.75e+00
  angle pdb=" CA  CYS A 472 "
        pdb=" CB  CYS A 472 "
        pdb=" SG  CYS A 472 "
      ideal   model   delta    sigma   weight residual
     114.40  121.35   -6.95 2.30e+00 1.89e-01 9.12e+00
  ... (remaining 16909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 6776
       17.70 -    35.41: 600
       35.41 -    53.11: 82
       53.11 -    70.81: 26
       70.81 -    88.52: 17
  Dihedral angle restraints: 7501
    sinusoidal: 3085
      harmonic: 4416
  Sorted by residual:
  dihedral pdb=" CB  CYS A 575 "
           pdb=" SG  CYS A 575 "
           pdb=" SG  CYS A 656 "
           pdb=" CB  CYS A 656 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.34  -52.34     1      1.00e+01 1.00e-02 3.73e+01
  dihedral pdb=" CB  CYS A 994 "
           pdb=" SG  CYS A 994 "
           pdb=" SG  CYS A1020 "
           pdb=" CB  CYS A1020 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.99   46.01     1      1.00e+01 1.00e-02 2.93e+01
  dihedral pdb=" CB  CYS A 472 "
           pdb=" SG  CYS A 472 "
           pdb=" SG  CYS A 498 "
           pdb=" CB  CYS A 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.59   45.41     1      1.00e+01 1.00e-02 2.86e+01
  ... (remaining 7498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1174
       0.038 -    0.075: 403
       0.075 -    0.112: 156
       0.112 -    0.150: 50
       0.150 -    0.187: 6
  Chirality restraints: 1789
  Sorted by residual:
  chirality pdb=" CB  ILE A 604 "
            pdb=" CA  ILE A 604 "
            pdb=" CG1 ILE A 604 "
            pdb=" CG2 ILE A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" CB  ILE A1019 "
            pdb=" CA  ILE A1019 "
            pdb=" CG1 ILE A1019 "
            pdb=" CG2 ILE A1019 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.00e-01
  chirality pdb=" CA  PHE A1368 "
            pdb=" N   PHE A1368 "
            pdb=" C   PHE A1368 "
            pdb=" CB  PHE A1368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 1786 not shown)

  Planarity restraints: 2194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1493 "    0.017 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   TYR A1493 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR A1493 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A1494 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  20 "    0.037 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO A  21 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1337 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A1338 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A1338 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A1338 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2191 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 501
        2.71 -     3.26: 11655
        3.26 -     3.81: 17400
        3.81 -     4.35: 21212
        4.35 -     4.90: 37298
  Nonbonded interactions: 88066
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1267 "
            pdb=" O   ASN A1269 "
     model   vdw
     2.166 2.440
  nonbonded pdb=" OE1 GLU A 372 "
            pdb=" OG1 THR A 380 "
     model   vdw
     2.181 2.440
  nonbonded pdb=" OG  SER A  92 "
            pdb=" OE2 GLU A1494 "
     model   vdw
     2.185 2.440
  nonbonded pdb=" OD1 ASN A1215 "
            pdb=" NE2 HIS A1252 "
     model   vdw
     2.229 2.520
  nonbonded pdb=" O   ASN A 432 "
            pdb=" OG1 THR A 436 "
     model   vdw
     2.233 2.440
  ... (remaining 88061 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.880
  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:          8.550
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     34.860
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
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      :  0.003   0.047  12477  Z= 0.178
  Angle     :  0.682  10.961  16914  Z= 0.371
  Chirality :  0.047   0.187   1789
  Planarity :  0.005   0.055   2194
  Dihedral  : 13.998  88.518   4642
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.91 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.20), residues: 1503
  helix: -2.47 (0.65), residues: 42
  sheet: -0.11 (0.25), residues: 440
  loop : -2.88 (0.17), residues: 1021

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2540
  time to fit residues: 62.8173
Evaluate side-chains
  102 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.293 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.9551
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0470
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 117 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 71 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 136 optimal weight:    0.2980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
A 211 ASN
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1026 HIS
** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.102  12477  Z= 0.210
  Angle     :  0.661   8.000  16914  Z= 0.348
  Chirality :  0.048   0.261   1789
  Planarity :  0.005   0.058   2194
  Dihedral  :  5.808  26.380   1648
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.71 %
    Favored  : 86.29 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  6.83 %
    Favored  : 91.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.20), residues: 1503
  helix: -2.03 (0.73), residues: 48
  sheet: -0.04 (0.25), residues: 441
  loop : -2.86 (0.17), residues: 1014

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2214
  time to fit residues: 39.6726
Evaluate side-chains
  106 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 1.375 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1217
  time to fit residues: 4.8331
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 113 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 136 optimal weight:    0.4980
   chunk 147 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1496 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  12477  Z= 0.246
  Angle     :  0.684  10.985  16914  Z= 0.361
  Chirality :  0.048   0.269   1789
  Planarity :  0.005   0.059   2194
  Dihedral  :  5.971  34.652   1648
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.17 %
    Favored  : 86.83 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.17 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.88 (0.20), residues: 1503
  helix: -1.77 (0.74), residues: 48
  sheet: -0.17 (0.26), residues: 416
  loop : -2.91 (0.17), residues: 1039

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 9
  residues processed: 124
  average time/residue: 0.2515
  time to fit residues: 46.7405
Evaluate side-chains
  106 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.388 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1094
  time to fit residues: 3.6688
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    5.9990
   chunk 102 optimal weight:    0.7980
   chunk 70 optimal weight:   30.0000
   chunk 15 optimal weight:    0.0570
   chunk 65 optimal weight:    0.0870
   chunk 91 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9990
   chunk 144 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0020
   chunk 129 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3886

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107  12477  Z= 0.183
  Angle     :  0.621  14.619  16914  Z= 0.327
  Chirality :  0.047   0.265   1789
  Planarity :  0.005   0.054   2194
  Dihedral  :  5.659  31.376   1648
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.91 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.79 (0.20), residues: 1503
  helix: -1.61 (0.77), residues: 48
  sheet:  0.01 (0.26), residues: 400
  loop : -2.87 (0.17), residues: 1055

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 9
  residues processed: 119
  average time/residue: 0.2401
  time to fit residues: 43.5856
Evaluate side-chains
  108 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 1.323 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1222
  time to fit residues: 4.1394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    0.0670
   chunk 82 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 123 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 130 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  12477  Z= 0.192
  Angle     :  0.640  12.649  16914  Z= 0.336
  Chirality :  0.047   0.236   1789
  Planarity :  0.005   0.055   2194
  Dihedral  :  5.634  27.698   1648
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.44 %
    Favored  : 87.56 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.21 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.20), residues: 1503
  helix: -1.65 (0.76), residues: 48
  sheet:  0.11 (0.26), residues: 417
  loop : -2.90 (0.17), residues: 1038

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2317
  time to fit residues: 40.4530
Evaluate side-chains
  103 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 1.363 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1170
  time to fit residues: 3.5076
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 130 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 145 optimal weight:    7.9990
   chunk 120 optimal weight:    0.7980
   chunk 67 optimal weight:   20.0000
   chunk 12 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 139 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 845 ASN
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  12477  Z= 0.189
  Angle     :  0.631  12.627  16914  Z= 0.333
  Chirality :  0.047   0.203   1789
  Planarity :  0.005   0.054   2194
  Dihedral  :  5.619  31.747   1648
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.88 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.74 (0.20), residues: 1503
  helix: -1.75 (0.76), residues: 48
  sheet:  0.11 (0.26), residues: 420
  loop : -2.90 (0.17), residues: 1035

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2574
  time to fit residues: 43.3441
Evaluate side-chains
  101 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 1.351 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1412
  time to fit residues: 3.8418
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 144 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12477  Z= 0.197
  Angle     :  0.638  11.439  16914  Z= 0.338
  Chirality :  0.047   0.208   1789
  Planarity :  0.005   0.057   2194
  Dihedral  :  5.663  29.241   1648
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.55 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.75 (0.20), residues: 1503
  helix: -1.76 (0.75), residues: 48
  sheet:  0.10 (0.26), residues: 419
  loop : -2.91 (0.17), residues: 1036

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 10
  residues processed: 111
  average time/residue: 0.2392
  time to fit residues: 40.8038
Evaluate side-chains
  108 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 1.489 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1337
  time to fit residues: 5.1654
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 113 optimal weight:    0.9980
   chunk 131 optimal weight:    0.6980
   chunk 138 optimal weight:   10.0000
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12477  Z= 0.180
  Angle     :  0.633  10.282  16914  Z= 0.333
  Chirality :  0.047   0.206   1789
  Planarity :  0.005   0.055   2194
  Dihedral  :  5.615  31.012   1648
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.77 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 15.44 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.74 (0.20), residues: 1503
  helix: -1.83 (0.75), residues: 48
  sheet:  0.09 (0.26), residues: 420
  loop : -2.90 (0.17), residues: 1035

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 106
  average time/residue: 0.2379
  time to fit residues: 38.7803
Evaluate side-chains
  100 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 1.440 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1107
  time to fit residues: 2.5897
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    6.9990
   chunk 138 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9980
   chunk 121 optimal weight:    5.9990
   chunk 127 optimal weight:    0.0370
   chunk 88 optimal weight:    0.6980
   chunk 142 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  12477  Z= 0.155
  Angle     :  0.615   9.167  16914  Z= 0.322
  Chirality :  0.046   0.214   1789
  Planarity :  0.005   0.052   2194
  Dihedral  :  5.451  28.603   1648
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 15.74 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.20), residues: 1503
  helix: -1.76 (0.75), residues: 48
  sheet:  0.22 (0.26), residues: 406
  loop : -2.88 (0.17), residues: 1049

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 0.2365
  time to fit residues: 38.1441
Evaluate side-chains
  101 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 1.477 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1143
  time to fit residues: 2.3377
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:   20.0000
   chunk 99 optimal weight:    2.9990
   chunk 149 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 94 optimal weight:    0.3980
   chunk 126 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 GLN
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 HIS
** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  12477  Z= 0.382
  Angle     :  0.801  12.024  16914  Z= 0.423
  Chirality :  0.051   0.215   1789
  Planarity :  0.005   0.073   2194
  Dihedral  :  6.362  30.924   1648
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.50 %
    Favored  : 85.43 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 15.74 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.10 (0.20), residues: 1503
  helix: -2.11 (0.70), residues: 48
  sheet: -0.24 (0.26), residues: 393
  loop : -3.03 (0.16), residues: 1062

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

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

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3006 Ramachandran restraints generated.
    1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 108
  average time/residue: 0.2652
  time to fit residues: 42.9222
Evaluate side-chains
  101 residues out of total 1347 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.429 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1443
  time to fit residues: 3.0331
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 119 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 HIS
** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.192468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.145176 restraints weight = 17096.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 3.27
r_work: 0.3846 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12477  Z= 0.190
  Angle     :  0.670  10.360  16914  Z= 0.354
  Chirality :  0.047   0.227   1789
  Planarity :  0.005   0.059   2194
  Dihedral  :  5.948  29.505   1648
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.11 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 15.66 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.20), residues: 1503
  helix: -2.01 (0.72), residues: 48
  sheet: -0.04 (0.26), residues: 405
  loop : -3.01 (0.17), residues: 1050
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2667.36 seconds
wall clock time: 49 minutes 26.17 seconds (2966.17 seconds total)