Starting phenix.real_space_refine
on Fri Mar 15 08:34:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/03_2024/7syf_25524.pdb"
  }
  resolution = 4.2
  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=   0.016 sd=   0.092
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      72      5.16       5
     C    7024      2.51       5
     N    1942      2.21       5
     O    2070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   78": "NH1" <-> "NH2"
    Residue "A GLU  130": "OE1" <-> "OE2"
    Residue "A GLU  153": "OE1" <-> "OE2"
    Residue "A ARG  181": "NH1" <-> "NH2"
    Residue "A GLU  245": "OE1" <-> "OE2"
    Residue "A GLU  288": "OE1" <-> "OE2"
    Residue "A GLU  378": "OE1" <-> "OE2"
    Residue "A GLU  379": "OE1" <-> "OE2"
    Residue "A GLU  414": "OE1" <-> "OE2"
    Residue "A GLU  453": "OE1" <-> "OE2"
    Residue "A GLU  488": "OE1" <-> "OE2"
    Residue "A GLU  508": "OE1" <-> "OE2"
    Residue "A GLU  562": "OE1" <-> "OE2"
    Residue "A GLU  563": "OE1" <-> "OE2"
    Residue "A GLU  585": "OE1" <-> "OE2"
    Residue "A GLU  589": "OE1" <-> "OE2"
    Residue "A GLU  599": "OE1" <-> "OE2"
    Residue "A GLU  600": "OE1" <-> "OE2"
    Residue "A GLU  602": "OE1" <-> "OE2"
    Residue "A GLU  632": "OE1" <-> "OE2"
    Residue "A GLU  633": "OE1" <-> "OE2"
    Residue "A GLU  640": "OE1" <-> "OE2"
    Residue "A GLU  641": "OE1" <-> "OE2"
    Residue "A GLU  658": "OE1" <-> "OE2"
    Residue "A GLU  673": "OE1" <-> "OE2"
    Residue "A GLU  685": "OE1" <-> "OE2"
    Residue "A GLU  708": "OE1" <-> "OE2"
    Residue "A GLU  769": "OE1" <-> "OE2"
    Residue "A GLU  780": "OE1" <-> "OE2"
    Residue "A GLU  793": "OE1" <-> "OE2"
    Residue "A GLU  803": "OE1" <-> "OE2"
    Residue "A GLU  852": "OE1" <-> "OE2"
    Residue "A GLU  858": "OE1" <-> "OE2"
    Residue "A GLU  871": "OE1" <-> "OE2"
    Residue "A GLU  875": "OE1" <-> "OE2"
    Residue "A GLU  888": "OE1" <-> "OE2"
    Residue "A GLU  899": "OE1" <-> "OE2"
    Residue "A GLU  918": "OE1" <-> "OE2"
    Residue "A GLU  928": "OE1" <-> "OE2"
    Residue "A GLU  939": "OE1" <-> "OE2"
    Residue "A GLU  978": "OE1" <-> "OE2"
    Residue "A GLU 1071": "OE1" <-> "OE2"
    Residue "A GLU 1074": "OE1" <-> "OE2"
    Residue "A GLU 1247": "OE1" <-> "OE2"
    Residue "A GLU 1265": "OE1" <-> "OE2"
    Residue "A GLU 1280": "OE1" <-> "OE2"
    Residue "A GLU 1301": "OE1" <-> "OE2"
    Residue "A GLU 1340": "OE1" <-> "OE2"
    Residue "A GLU 1355": "OE1" <-> "OE2"
    Residue "A GLU 1357": "OE1" <-> "OE2"
    Residue "A GLU 1358": "OE1" <-> "OE2"
    Residue "A ARG 1365": "NH1" <-> "NH2"
    Residue "A GLU 1369": "OE1" <-> "OE2"
    Residue "A GLU 1397": "OE1" <-> "OE2"
    Residue "A GLU 1405": "OE1" <-> "OE2"
    Residue "A GLU 1431": "OE1" <-> "OE2"
    Residue "A GLU 1456": "OE1" <-> "OE2"
    Residue "A GLU 1473": "OE1" <-> "OE2"
    Residue "A GLU 1476": "OE1" <-> "OE2"
    Residue "A GLU 1487": "OE1" <-> "OE2"
    Residue "A GLU 1499": "OE1" <-> "OE2"
    Residue "A GLU 1514": "OE1" <-> "OE2"
    Residue "A ARG 1534": "NH1" <-> "NH2"
    Residue "A GLU 1541": "OE1" <-> "OE2"
    Residue "A GLU 1570": "OE1" <-> "OE2"
    Residue "A ARG 1621": "NH1" <-> "NH2"
    Residue "A GLU 1628": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 11108
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1391, 11108
          Classifications: {'peptide': 1391}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1340}
          Chain breaks: 7
  Time building chain proxies: 6.03, per 1000 atoms: 0.54
  Number of scatterers: 11108
  At special positions: 0
  Unit cell: (111.688, 123.799, 139.947, 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      72     16.00
     O    2070      8.00
     N    1942      7.00
     C    7024      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: 3.40
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      58.6% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 82
      removed outlier: 3.715A  pdb=" N   HIS A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASN A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 3.511A  pdb=" N   SER A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ASN A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 143
      removed outlier: 4.282A  pdb=" N   ASP A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LYS A 141 " --> pdb=" O   LYS A 137 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS A 143 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 165
      removed outlier: 3.780A  pdb=" N   TYR A 148 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLU A 153 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   LYS A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 180
      removed outlier: 3.673A  pdb=" N   MET A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 193 through 213
      Proline residue:  A 203  - end of helix
      removed outlier: 3.667A  pdb=" N   ARG A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 237
      removed outlier: 4.610A  pdb=" N   ALA A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 256
      removed outlier: 3.709A  pdb=" N   LEU A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 269
      removed outlier: 3.646A  pdb=" N   ILE A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 421
    Processing helix  chain 'A' and resid 444 through 454
    Processing helix  chain 'A' and resid 459 through 473
      removed outlier: 3.539A  pdb=" N   GLY A 463 " --> pdb=" O   LYS A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 523
      removed outlier: 3.512A  pdb=" N   ASP A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE A 510 " --> pdb=" O   GLU A 506 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   MET A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 555
    Processing helix  chain 'A' and resid 560 through 574
    Processing helix  chain 'A' and resid 596 through 603
      removed outlier: 3.906A  pdb=" N   MET A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 610
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 675 through 679
    Processing helix  chain 'A' and resid 680 through 694
      removed outlier: 3.515A  pdb=" N   SER A 686 " --> pdb=" O   SER A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 744
    Processing helix  chain 'A' and resid 763 through 769
    Processing helix  chain 'A' and resid 771 through 778
    Processing helix  chain 'A' and resid 779 through 782
      removed outlier: 4.135A  pdb=" N   LEU A 782 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 779 through 782'
    Processing helix  chain 'A' and resid 791 through 806
    Processing helix  chain 'A' and resid 878 through 908
    Processing helix  chain 'A' and resid 913 through 946
    Processing helix  chain 'A' and resid 963 through 968
    Processing helix  chain 'A' and resid 1064 through 1068
    Processing helix  chain 'A' and resid 1069 through 1108
      removed outlier: 3.622A  pdb=" N   ARG A1073 " --> pdb=" O   LYS A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1237
      removed outlier: 4.925A  pdb=" N   LEU A1235 " --> pdb=" O   SER A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1238 through 1248
    Processing helix  chain 'A' and resid 1256 through 1263
    Processing helix  chain 'A' and resid 1263 through 1281
    Processing helix  chain 'A' and resid 1284 through 1315
    Processing helix  chain 'A' and resid 1316 through 1346
    Processing helix  chain 'A' and resid 1353 through 1357
      removed outlier: 3.565A  pdb=" N   GLU A1357 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1375
    Processing helix  chain 'A' and resid 1389 through 1407
      removed outlier: 4.241A  pdb=" N   VAL A1401 " --> pdb=" O   GLU A1397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1444 through 1450
    Processing helix  chain 'A' and resid 1452 through 1457
    Processing helix  chain 'A' and resid 1480 through 1517
    Processing helix  chain 'A' and resid 1521 through 1551
      removed outlier: 4.216A  pdb=" N   ARG A1534 " --> pdb=" O   ASP A1530 " (cutoff:3.500A)
      Proline residue:  A1535  - end of helix
    Processing helix  chain 'A' and resid 1563 through 1576
    Processing helix  chain 'A' and resid 1588 through 1606
    Processing helix  chain 'A' and resid 1609 through 1611
      No H-bonds generated for 'chain 'A' and resid 1609 through 1611'
    Processing helix  chain 'A' and resid 1612 through 1624
    Processing helix  chain 'A' and resid 1626 through 1631
      removed outlier: 4.133A  pdb=" N   LEU A1630 " --> pdb=" O   ARG A1626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 258
      removed outlier: 3.559A  pdb=" N   PHE A 327 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   PHE A 327 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LYS A 302 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   GLN A 287 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LEU A 279 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ARG A 289 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR A 277 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   PHE A 291 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   GLN A 275 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431
      removed outlier: 5.299A  pdb=" N   LYS A 429 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A 440 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 8.715A  pdb=" N   LYS A 440 " --> pdb=" O   PHE A 494 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   PHE A 494 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 533
      removed outlier: 5.048A  pdb=" N   ARG A 532 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   LYS A 540 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   SER A 541 " --> pdb=" O   PHE A 595 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   PHE A 595 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 671
      removed outlier: 6.337A  pdb=" N   LEU A 701 " --> pdb=" O   TYR A 669 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ILE A 671 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ARG A 699 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   PHE A 615 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL A 860 " --> pdb=" O   PHE A 615 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   LEU A 617 " --> pdb=" O   GLU A 858 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   GLU A 858 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU A 619 " --> pdb=" O   VAL A 856 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   HIS A 868 " --> pdb=" O   SER A 980 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLN A1579 " --> pdb=" O   CYS A1021 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   CYS A1583 " --> pdb=" O   MET A1025 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A1376 " --> pdb=" O   HIS A1464 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ALA A1466 " --> pdb=" O   VAL A1376 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A1378 " --> pdb=" O   ALA A1466 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   PHE A1468 " --> pdb=" O   LEU A1378 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   CYS A1380 " --> pdb=" O   PHE A1468 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR A1410 " --> pdb=" O   VAL A1439 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   PHE A1441 " --> pdb=" O   THR A1410 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   SER A1412 " --> pdb=" O   PHE A1441 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU A1443 " --> pdb=" O   SER A1412 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LYS A1414 " --> pdb=" O   LEU A1443 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 642
      removed outlier: 6.651A  pdb=" N   ASP A 638 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 713
      removed outlier: 6.485A  pdb=" N   THR A 843 " --> pdb=" O   VAL A 754 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   VAL A 754 " --> pdb=" O   THR A 843 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR A 845 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 721 through 724
      removed outlier: 6.672A  pdb=" N   GLN A 722 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    2007 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: 4.15

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2166
        1.32 -     1.45: 2626
        1.45 -     1.57: 6413
        1.57 -     1.70: 0
        1.70 -     1.83: 105
  Bond restraints: 11310
  Sorted by residual:
  bond pdb=" C   PHE A1260 "
       pdb=" N   LYS A1261 "
    ideal  model  delta    sigma   weight residual
    1.335  1.571 -0.237 1.25e-02 6.40e+03 3.59e+02
  bond pdb=" C   ARG A 181 "
       pdb=" N   LYS A 182 "
    ideal  model  delta    sigma   weight residual
    1.331  1.490 -0.159 1.42e-02 4.96e+03 1.25e+02
  bond pdb=" C   GLU A 619 "
       pdb=" N   ASN A 620 "
    ideal  model  delta    sigma   weight residual
    1.330  1.253  0.077 1.38e-02 5.25e+03 3.14e+01
  bond pdb=" C   VAL A 618 "
       pdb=" N   GLU A 619 "
    ideal  model  delta    sigma   weight residual
    1.332  1.260  0.072 1.40e-02 5.10e+03 2.66e+01
  bond pdb=" C   LEU A 227 "
       pdb=" N   GLN A 228 "
    ideal  model  delta    sigma   weight residual
    1.335  1.387 -0.053 1.31e-02 5.83e+03 1.61e+01
  ... (remaining 11305 not shown)

  Histogram of bond angle deviations from ideal:
       96.93 -   104.61: 153
      104.61 -   112.30: 4866
      112.30 -   119.98: 5401
      119.98 -   127.67: 4763
      127.67 -   135.35: 79
  Bond angle restraints: 15262
  Sorted by residual:
  angle pdb=" C   PHE A1260 "
        pdb=" N   LYS A1261 "
        pdb=" CA  LYS A1261 "
      ideal   model   delta    sigma   weight residual
     120.54  109.71   10.83 1.35e+00 5.49e-01 6.44e+01
  angle pdb=" N   TYR A 539 "
        pdb=" CA  TYR A 539 "
        pdb=" C   TYR A 539 "
      ideal   model   delta    sigma   weight residual
     109.95   99.43   10.52 1.59e+00 3.96e-01 4.38e+01
  angle pdb=" CA  PHE A  70 "
        pdb=" CB  PHE A  70 "
        pdb=" CG  PHE A  70 "
      ideal   model   delta    sigma   weight residual
     113.80  120.01   -6.21 1.00e+00 1.00e+00 3.86e+01
  angle pdb=" N   ILE A 103 "
        pdb=" CA  ILE A 103 "
        pdb=" CB  ILE A 103 "
      ideal   model   delta    sigma   weight residual
     110.51  117.25   -6.74 1.11e+00 8.12e-01 3.69e+01
  angle pdb=" O   PHE A1260 "
        pdb=" C   PHE A1260 "
        pdb=" N   LYS A1261 "
      ideal   model   delta    sigma   weight residual
     122.12  128.45   -6.33 1.06e+00 8.90e-01 3.57e+01
  ... (remaining 15257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 6298
       17.72 -    35.44: 481
       35.44 -    53.15: 99
       53.15 -    70.87: 35
       70.87 -    88.59: 11
  Dihedral angle restraints: 6924
    sinusoidal: 2859
      harmonic: 4065
  Sorted by residual:
  dihedral pdb=" CA  LEU A1068 "
           pdb=" C   LEU A1068 "
           pdb=" N   LYS A1069 "
           pdb=" CA  LYS A1069 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.57   29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  LEU A 700 "
           pdb=" C   LEU A 700 "
           pdb=" N   LEU A 701 "
           pdb=" CA  LEU A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.98   29.02     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  ALA A 283 "
           pdb=" C   ALA A 283 "
           pdb=" N   GLY A 284 "
           pdb=" CA  GLY A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.65  -28.35     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 6921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1210
       0.098 -    0.196: 426
       0.196 -    0.294: 56
       0.294 -    0.392: 11
       0.392 -    0.490: 6
  Chirality restraints: 1709
  Sorted by residual:
  chirality pdb=" CA  ILE A 103 "
            pdb=" N   ILE A 103 "
            pdb=" C   ILE A 103 "
            pdb=" CB  ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.94    0.49 2.00e-01 2.50e+01 6.00e+00
  chirality pdb=" CA  ARG A 303 "
            pdb=" N   ARG A 303 "
            pdb=" C   ARG A 303 "
            pdb=" CB  ARG A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.73e+00
  chirality pdb=" CA  ARG A 198 "
            pdb=" N   ARG A 198 "
            pdb=" C   ARG A 198 "
            pdb=" CB  ARG A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.26e+00
  ... (remaining 1706 not shown)

  Planarity restraints: 1973
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 260 "   -0.134 2.00e-02 2.50e+03   7.38e-02 1.36e+02
        pdb=" CG  TRP A 260 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 260 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 260 "    0.108 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 260 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 260 "    0.038 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 260 "    0.102 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 260 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 260 "   -0.020 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 260 "   -0.101 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 787 "   -0.093 2.00e-02 2.50e+03   5.11e-02 6.52e+01
        pdb=" CG  TRP A 787 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 787 "    0.051 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 787 "    0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 787 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 787 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 787 "    0.074 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 787 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 787 "    0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 787 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1020 "    0.084 2.00e-02 2.50e+03   6.25e-02 5.85e+01
        pdb=" CG  HIS A1020 "   -0.095 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1020 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1020 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1020 "    0.034 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1020 "    0.055 2.00e-02 2.50e+03
  ... (remaining 1970 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 4664
        2.95 -     3.44: 11727
        3.44 -     3.92: 18891
        3.92 -     4.41: 21061
        4.41 -     4.90: 34498
  Nonbonded interactions: 90841
  Sorted by model distance:
  nonbonded pdb=" N   TYR A 539 "
            pdb=" O   TYR A 539 "
     model   vdw
     2.460 2.496
  nonbonded pdb=" OG  SER A 458 "
            pdb=" OE2 GLU A 462 "
     model   vdw
     2.478 2.440
  nonbonded pdb=" OG  SER A1569 "
            pdb=" OE2 GLU A1597 "
     model   vdw
     2.512 2.440
  nonbonded pdb=" ND1 HIS A  77 "
            pdb=" NH2 ARG A  80 "
     model   vdw
     2.520 3.200
  nonbonded pdb=" OG1 THR A 354 "
            pdb=" OE1 GLU A1092 "
     model   vdw
     2.564 2.440
  ... (remaining 90836 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:             0.180
  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:          1.440
  Check model and map are aligned:         0.160
  Set scattering table:                    0.100
  Process input model:                     28.860
  Find NCS groups from input model:        0.400
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
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      :  0.013   0.237  11310  Z= 0.829
  Angle     :  1.861  10.834  15262  Z= 1.269
  Chirality :  0.098   0.490   1709
  Planarity :  0.015   0.128   1973
  Dihedral  : 14.320  88.585   4288
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  3.60 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.61 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -1.56 (0.20), residues: 1375
  helix: -1.07 (0.15), residues: 766
  sheet: -0.80 (0.39), residues: 153
  loop : -0.65 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.134   0.032   TRP A 260 
 HIS   0.019   0.005   HIS A 579 
 PHE   0.067   0.014   PHE A 593 
 TYR   0.097   0.016   TYR A 191 
 ARG   0.009   0.001   ARG A 212 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  425 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 409
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8209 (pp30)
REVERT: A  104 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8566 (pt0)
REVERT: A  112 ASP cc_start: 0.8719 (m-30) cc_final: 0.8507 (t0)
REVERT: A  144 VAL cc_start: 0.8328 (m) cc_final: 0.7645 (p)
REVERT: A  176 MET cc_start: 0.6393 (mtm) cc_final: 0.5915 (ttt)
REVERT: A  177 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.1563 (mt)
REVERT: A  230 MET cc_start: 0.7197 (mmp) cc_final: 0.6594 (mmp)
REVERT: A  292 PHE cc_start: 0.6897 (m-80) cc_final: 0.6467 (m-80)
REVERT: A  359 TRP cc_start: 0.6886 (p90) cc_final: 0.6224 (p90)
REVERT: A  370 PHE cc_start: 0.7952 (p90) cc_final: 0.7621 (p90)
REVERT: A  510 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5527 (tt)
REVERT: A  511 MET cc_start: 0.5830 (mpp) cc_final: 0.4848 (mpp)
REVERT: A  539 TYR cc_start: 0.7354 (m-80) cc_final: 0.6967 (m-80)
REVERT: A  591 GLN cc_start: 0.7824 (mt0) cc_final: 0.6737 (tt0)
REVERT: A  598 ASP cc_start: 0.8273 (m-30) cc_final: 0.7583 (m-30)
REVERT: A  622 LEU cc_start: 0.7602 (tp) cc_final: 0.7060 (tp)
REVERT: A  631 GLN cc_start: 0.7013 (mt0) cc_final: 0.6457 (mt0)
REVERT: A  691 SER cc_start: 0.6742 (m) cc_final: 0.6485 (p)
REVERT: A  701 LEU cc_start: 0.7785 (mt) cc_final: 0.7475 (mm)
REVERT: A  741 MET cc_start: 0.7502 (ttm) cc_final: 0.6183 (ttm)
REVERT: A  768 LEU cc_start: 0.8776 (mt) cc_final: 0.8521 (mt)
REVERT: A  770 HIS cc_start: 0.8372 (m-70) cc_final: 0.7852 (m-70)
REVERT: A  900 ASN cc_start: 0.8730 (m-40) cc_final: 0.8324 (t0)
REVERT: A  915 PRO cc_start: 0.6507 (Cg_exo) cc_final: 0.5512 (Cg_endo)
REVERT: A  919 PHE cc_start: 0.7522 (t80) cc_final: 0.7114 (t80)
REVERT: A  922 ILE cc_start: 0.8722 (mt) cc_final: 0.8076 (mt)
REVERT: A  923 CYS cc_start: 0.7634 (m) cc_final: 0.6920 (m)
REVERT: A  924 ASP cc_start: 0.8929 (m-30) cc_final: 0.8714 (m-30)
REVERT: A  925 THR cc_start: 0.8956 (m) cc_final: 0.8750 (p)
REVERT: A  926 LYS cc_start: 0.8618 (mttt) cc_final: 0.8282 (mttt)
REVERT: A  928 GLU cc_start: 0.8744 (tt0) cc_final: 0.8490 (tt0)
REVERT: A  929 SER cc_start: 0.9131 (t) cc_final: 0.8915 (p)
REVERT: A  932 GLN cc_start: 0.8093 (mt0) cc_final: 0.7501 (tp-100)
REVERT: A  936 CYS cc_start: 0.8731 (m) cc_final: 0.7422 (m)
REVERT: A  939 GLU cc_start: 0.7806 (tp30) cc_final: 0.6874 (tp30)
REVERT: A  940 PHE cc_start: 0.8560 (m-10) cc_final: 0.7669 (m-10)
REVERT: A  943 GLN cc_start: 0.7534 (mt0) cc_final: 0.6308 (mt0)
REVERT: A 1079 TYR cc_start: 0.6817 (m-10) cc_final: 0.6307 (m-10)
REVERT: A 1104 LEU cc_start: 0.6206 (mt) cc_final: 0.5570 (tt)
REVERT: A 1214 LYS cc_start: 0.8444 (mttt) cc_final: 0.7990 (mtmm)
REVERT: A 1324 ASP cc_start: 0.8176 (m-30) cc_final: 0.7700 (m-30)
REVERT: A 1328 CYS cc_start: 0.6946 (t) cc_final: 0.6187 (t)
REVERT: A 1332 VAL cc_start: 0.9021 (t) cc_final: 0.8336 (t)
REVERT: A 1339 SER cc_start: 0.9047 (t) cc_final: 0.8674 (p)
REVERT: A 1343 LEU cc_start: 0.8889 (mt) cc_final: 0.8673 (mm)
REVERT: A 1353 ASN cc_start: 0.6419 (m-40) cc_final: 0.6006 (m-40)
REVERT: A 1366 LYS cc_start: 0.8935 (mttt) cc_final: 0.8546 (mttt)
REVERT: A 1369 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8224 (mt-10)
REVERT: A 1378 LEU cc_start: 0.7679 (tp) cc_final: 0.7399 (tp)
REVERT: A 1384 LEU cc_start: 0.8469 (mt) cc_final: 0.7496 (mp)
REVERT: A 1414 LYS cc_start: 0.7917 (mttt) cc_final: 0.7283 (mmmm)
REVERT: A 1428 TYR cc_start: 0.7256 (m-80) cc_final: 0.6753 (m-80)
REVERT: A 1438 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8072 (ttpp)
REVERT: A 1441 PHE cc_start: 0.8074 (m-80) cc_final: 0.6516 (m-80)
REVERT: A 1504 TYR cc_start: 0.8498 (t80) cc_final: 0.8224 (t80)
REVERT: A 1507 LYS cc_start: 0.8570 (mttt) cc_final: 0.8259 (tptt)
REVERT: A 1508 LEU cc_start: 0.8727 (tp) cc_final: 0.7579 (tp)
REVERT: A 1512 TYR cc_start: 0.7252 (m-80) cc_final: 0.6748 (m-80)
REVERT: A 1530 ASP cc_start: 0.6688 (m-30) cc_final: 0.6472 (m-30)
REVERT: A 1531 GLN cc_start: 0.8564 (mt0) cc_final: 0.7799 (mm110)
REVERT: A 1536 ILE cc_start: 0.8915 (mt) cc_final: 0.8461 (tp)
REVERT: A 1542 LEU cc_start: 0.9254 (mt) cc_final: 0.8986 (mt)
REVERT: A 1546 MET cc_start: 0.8415 (tpp) cc_final: 0.8097 (mmm)
REVERT: A 1593 SER cc_start: 0.7864 (t) cc_final: 0.7654 (p)
REVERT: A 1605 SER cc_start: 0.8432 (m) cc_final: 0.7977 (p)
REVERT: A 1633 ASN cc_start: 0.8377 (m-40) cc_final: 0.7311 (m-40)
  outliers start: 16
  outliers final: 3
  residues processed: 418
  average time/residue: 0.2924
  time to fit residues: 160.8637
Evaluate side-chains
  295 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 290
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
A 110 HIS
A 133 ASN
A 228 GLN
A 256 HIS
A 393 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 HIS
A 522 HIS
** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
A 770 HIS
A 790 HIS
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
A1379 HIS
A1415 GLN
** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11310  Z= 0.256
  Angle     :  0.671   9.427  15262  Z= 0.364
  Chirality :  0.043   0.264   1709
  Planarity :  0.006   0.122   1973
  Dihedral  :  6.100  76.096   1510
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.47 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.41 (0.22), residues: 1375
  helix:  0.85 (0.18), residues: 770
  sheet: -0.63 (0.37), residues: 167
  loop : -0.18 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 369 
 HIS   0.008   0.002   HIS A 110 
 PHE   0.025   0.002   PHE A  70 
 TYR   0.025   0.002   TYR A1096 
 ARG   0.013   0.001   ARG A1393 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 321
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.7228 (mp) cc_final: 0.6818 (pp)
REVERT: A   72 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8190 (pp30)
REVERT: A  104 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8460 (mp0)
REVERT: A  108 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8044 (pm20)
REVERT: A  176 MET cc_start: 0.6881 (mtm) cc_final: 0.6416 (ttt)
REVERT: A  202 TYR cc_start: 0.7513 (m-10) cc_final: 0.7200 (m-10)
REVERT: A  359 TRP cc_start: 0.6303 (p90) cc_final: 0.6094 (p90)
REVERT: A  468 GLN cc_start: 0.6759 (tp40) cc_final: 0.6022 (pp30)
REVERT: A  532 ARG cc_start: 0.2727 (tpt170) cc_final: 0.1993 (tpm170)
REVERT: A  539 TYR cc_start: 0.7557 (m-80) cc_final: 0.7074 (m-80)
REVERT: A  547 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6841 (tppt)
REVERT: A  586 PHE cc_start: 0.7188 (t80) cc_final: 0.6619 (t80)
REVERT: A  598 ASP cc_start: 0.8067 (m-30) cc_final: 0.7476 (m-30)
REVERT: A  613 ASN cc_start: 0.8243 (m110) cc_final: 0.7988 (m-40)
REVERT: A  691 SER cc_start: 0.7254 (m) cc_final: 0.6871 (p)
REVERT: A  770 HIS cc_start: 0.8370 (m90) cc_final: 0.7974 (m90)
REVERT: A  922 ILE cc_start: 0.8727 (mt) cc_final: 0.8058 (mt)
REVERT: A  926 LYS cc_start: 0.8437 (mttt) cc_final: 0.8117 (mttt)
REVERT: A  928 GLU cc_start: 0.8647 (tt0) cc_final: 0.8351 (tt0)
REVERT: A  932 GLN cc_start: 0.7824 (mt0) cc_final: 0.7529 (tp40)
REVERT: A  936 CYS cc_start: 0.8511 (m) cc_final: 0.7931 (m)
REVERT: A  939 GLU cc_start: 0.7540 (tp30) cc_final: 0.6502 (tp30)
REVERT: A  940 PHE cc_start: 0.8507 (m-10) cc_final: 0.7444 (m-10)
REVERT: A  943 GLN cc_start: 0.7384 (mt0) cc_final: 0.6181 (mt0)
REVERT: A 1023 THR cc_start: 0.7278 (m) cc_final: 0.6667 (p)
REVERT: A 1079 TYR cc_start: 0.6879 (m-10) cc_final: 0.6494 (m-10)
REVERT: A 1104 LEU cc_start: 0.6190 (mt) cc_final: 0.5884 (tp)
REVERT: A 1214 LYS cc_start: 0.8393 (mttt) cc_final: 0.7782 (pttm)
REVERT: A 1233 ASN cc_start: 0.7447 (m110) cc_final: 0.7130 (m110)
REVERT: A 1250 HIS cc_start: 0.7116 (m-70) cc_final: 0.6911 (m90)
REVERT: A 1296 ILE cc_start: 0.9182 (mt) cc_final: 0.8967 (pt)
REVERT: A 1320 GLN cc_start: 0.8382 (tp40) cc_final: 0.7688 (tp40)
REVERT: A 1324 ASP cc_start: 0.7617 (m-30) cc_final: 0.7267 (m-30)
REVERT: A 1332 VAL cc_start: 0.9030 (t) cc_final: 0.8645 (t)
REVERT: A 1338 PHE cc_start: 0.8483 (t80) cc_final: 0.8259 (t80)
REVERT: A 1339 SER cc_start: 0.9083 (t) cc_final: 0.8529 (p)
REVERT: A 1343 LEU cc_start: 0.8798 (mt) cc_final: 0.8286 (pp)
REVERT: A 1366 LYS cc_start: 0.9077 (mttt) cc_final: 0.8663 (mttt)
REVERT: A 1369 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8111 (mt-10)
REVERT: A 1377 LEU cc_start: 0.8206 (tp) cc_final: 0.7974 (tp)
REVERT: A 1384 LEU cc_start: 0.8402 (mt) cc_final: 0.8091 (mt)
REVERT: A 1403 LEU cc_start: 0.8128 (mt) cc_final: 0.7848 (mp)
REVERT: A 1428 TYR cc_start: 0.7177 (m-80) cc_final: 0.6739 (m-80)
REVERT: A 1438 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7791 (ttpp)
REVERT: A 1441 PHE cc_start: 0.7986 (m-80) cc_final: 0.7030 (m-10)
REVERT: A 1488 ASP cc_start: 0.7121 (m-30) cc_final: 0.6875 (m-30)
REVERT: A 1508 LEU cc_start: 0.8874 (tp) cc_final: 0.7629 (tp)
REVERT: A 1512 TYR cc_start: 0.6948 (m-80) cc_final: 0.6676 (m-80)
REVERT: A 1530 ASP cc_start: 0.6531 (m-30) cc_final: 0.6284 (m-30)
REVERT: A 1531 GLN cc_start: 0.8579 (mt0) cc_final: 0.7763 (mm110)
REVERT: A 1546 MET cc_start: 0.8383 (tpp) cc_final: 0.8109 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 321
  average time/residue: 0.2709
  time to fit residues: 119.6341
Evaluate side-chains
  262 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 85 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 112 optimal weight:    8.9990
   chunk 125 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 243 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 GLN
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1095 GLN
A1284 ASN
A1287 ASN
** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11310  Z= 0.248
  Angle     :  0.645   9.871  15262  Z= 0.344
  Chirality :  0.042   0.256   1709
  Planarity :  0.005   0.052   1973
  Dihedral  :  5.735  76.168   1510
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.84 (0.23), residues: 1375
  helix:  1.26 (0.18), residues: 772
  sheet: -0.60 (0.37), residues: 154
  loop : -0.09 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A1367 
 HIS   0.006   0.001   HIS A1020 
 PHE   0.023   0.002   PHE A1226 
 TYR   0.017   0.002   TYR A1504 
 ARG   0.008   0.001   ARG A1454 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8269 (mp0)
REVERT: A  176 MET cc_start: 0.7081 (mtm) cc_final: 0.6636 (ttt)
REVERT: A  192 LEU cc_start: 0.8511 (mt) cc_final: 0.8156 (tp)
REVERT: A  202 TYR cc_start: 0.7464 (m-10) cc_final: 0.7203 (m-10)
REVERT: A  264 ASN cc_start: 0.7555 (t0) cc_final: 0.7345 (t0)
REVERT: A  359 TRP cc_start: 0.6317 (p90) cc_final: 0.5719 (p90)
REVERT: A  539 TYR cc_start: 0.7479 (m-80) cc_final: 0.6933 (m-80)
REVERT: A  567 LEU cc_start: 0.7161 (mt) cc_final: 0.6902 (pp)
REVERT: A  598 ASP cc_start: 0.7964 (m-30) cc_final: 0.7259 (m-30)
REVERT: A  643 ASN cc_start: 0.8218 (m-40) cc_final: 0.7981 (m110)
REVERT: A  663 GLN cc_start: 0.5377 (tm-30) cc_final: 0.5174 (tm-30)
REVERT: A  691 SER cc_start: 0.7274 (m) cc_final: 0.6841 (p)
REVERT: A  695 ARG cc_start: 0.7818 (mmp80) cc_final: 0.7481 (mmp-170)
REVERT: A  741 MET cc_start: 0.7747 (mtt) cc_final: 0.7121 (mtt)
REVERT: A  770 HIS cc_start: 0.8327 (m90) cc_final: 0.8011 (m90)
REVERT: A  841 MET cc_start: 0.7049 (mmt) cc_final: 0.6380 (mmm)
REVERT: A  859 TYR cc_start: 0.7728 (p90) cc_final: 0.7403 (p90)
REVERT: A  926 LYS cc_start: 0.8378 (mttt) cc_final: 0.8167 (mttt)
REVERT: A  928 GLU cc_start: 0.8604 (tt0) cc_final: 0.8383 (tt0)
REVERT: A  932 GLN cc_start: 0.7851 (mt0) cc_final: 0.7556 (tp40)
REVERT: A  936 CYS cc_start: 0.8491 (m) cc_final: 0.7912 (m)
REVERT: A  939 GLU cc_start: 0.7540 (tp30) cc_final: 0.6846 (tp30)
REVERT: A  953 LYS cc_start: 0.7783 (tttt) cc_final: 0.7533 (tttt)
REVERT: A 1015 MET cc_start: 0.5539 (mpp) cc_final: 0.4829 (mpp)
REVERT: A 1023 THR cc_start: 0.7276 (m) cc_final: 0.6942 (p)
REVERT: A 1079 TYR cc_start: 0.6829 (m-10) cc_final: 0.6437 (m-10)
REVERT: A 1104 LEU cc_start: 0.6533 (mt) cc_final: 0.6152 (tp)
REVERT: A 1214 LYS cc_start: 0.8390 (mttt) cc_final: 0.7872 (pttm)
REVERT: A 1233 ASN cc_start: 0.7362 (m110) cc_final: 0.7061 (m-40)
REVERT: A 1296 ILE cc_start: 0.9198 (mt) cc_final: 0.8945 (pt)
REVERT: A 1320 GLN cc_start: 0.8311 (tp40) cc_final: 0.7794 (tp40)
REVERT: A 1324 ASP cc_start: 0.7848 (m-30) cc_final: 0.7348 (m-30)
REVERT: A 1332 VAL cc_start: 0.9101 (t) cc_final: 0.8790 (t)
REVERT: A 1338 PHE cc_start: 0.8555 (t80) cc_final: 0.8339 (t80)
REVERT: A 1339 SER cc_start: 0.9013 (t) cc_final: 0.8554 (p)
REVERT: A 1346 LEU cc_start: 0.9073 (mt) cc_final: 0.8845 (mt)
REVERT: A 1353 ASN cc_start: 0.6332 (m-40) cc_final: 0.6093 (m-40)
REVERT: A 1384 LEU cc_start: 0.8467 (mt) cc_final: 0.8223 (mt)
REVERT: A 1392 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6979 (mm-30)
REVERT: A 1403 LEU cc_start: 0.8071 (mt) cc_final: 0.7791 (mp)
REVERT: A 1502 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8222 (tp-100)
REVERT: A 1508 LEU cc_start: 0.8957 (tp) cc_final: 0.7626 (tp)
REVERT: A 1512 TYR cc_start: 0.7004 (m-80) cc_final: 0.6773 (m-80)
REVERT: A 1530 ASP cc_start: 0.6657 (m-30) cc_final: 0.6406 (m-30)
REVERT: A 1531 GLN cc_start: 0.8652 (mt0) cc_final: 0.7875 (mm110)
REVERT: A 1619 ILE cc_start: 0.5572 (mm) cc_final: 0.5345 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.2586
  time to fit residues: 108.0752
Evaluate side-chains
  257 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9990
   chunk 126 optimal weight:    5.9990
   chunk 134 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1537 ASN
A1633 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6411
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11310  Z= 0.208
  Angle     :  0.596   8.147  15262  Z= 0.314
  Chirality :  0.041   0.237   1709
  Planarity :  0.004   0.077   1973
  Dihedral  :  5.552  75.578   1510
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.99 (0.23), residues: 1375
  helix:  1.39 (0.18), residues: 778
  sheet: -0.56 (0.38), residues: 151
  loop : -0.05 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1367 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.022   0.002   PHE A1226 
 TYR   0.020   0.002   TYR A1428 
 ARG   0.005   0.000   ARG A1621 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8434 (mp0)
REVERT: A  108 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8265 (mm-30)
REVERT: A  175 CYS cc_start: 0.8394 (m) cc_final: 0.8189 (m)
REVERT: A  176 MET cc_start: 0.6887 (mtm) cc_final: 0.6461 (ttt)
REVERT: A  202 TYR cc_start: 0.7479 (m-10) cc_final: 0.7167 (m-10)
REVERT: A  257 ILE cc_start: 0.7188 (mt) cc_final: 0.6858 (mt)
REVERT: A  264 ASN cc_start: 0.7612 (t0) cc_final: 0.7299 (t0)
REVERT: A  343 ASP cc_start: 0.8222 (m-30) cc_final: 0.8016 (t0)
REVERT: A  359 TRP cc_start: 0.5688 (p90) cc_final: 0.5175 (p90)
REVERT: A  360 LYS cc_start: 0.7775 (tmtt) cc_final: 0.6942 (ptpp)
REVERT: A  430 ASP cc_start: 0.7573 (t0) cc_final: 0.7338 (m-30)
REVERT: A  539 TYR cc_start: 0.7464 (m-80) cc_final: 0.6913 (m-80)
REVERT: A  540 LYS cc_start: 0.8266 (mttp) cc_final: 0.8006 (pttm)
REVERT: A  563 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: A  591 GLN cc_start: 0.7596 (mt0) cc_final: 0.7297 (mt0)
REVERT: A  598 ASP cc_start: 0.7886 (m-30) cc_final: 0.7119 (m-30)
REVERT: A  691 SER cc_start: 0.7199 (m) cc_final: 0.6824 (p)
REVERT: A  708 GLU cc_start: 0.6842 (tp30) cc_final: 0.6566 (tp30)
REVERT: A  741 MET cc_start: 0.7861 (mtt) cc_final: 0.7472 (mtt)
REVERT: A  770 HIS cc_start: 0.8282 (m90) cc_final: 0.8003 (m90)
REVERT: A  792 HIS cc_start: 0.7628 (t-170) cc_final: 0.7262 (t70)
REVERT: A  859 TYR cc_start: 0.7687 (p90) cc_final: 0.7361 (p90)
REVERT: A  928 GLU cc_start: 0.8615 (tt0) cc_final: 0.8357 (tt0)
REVERT: A  932 GLN cc_start: 0.7855 (mt0) cc_final: 0.7500 (tp40)
REVERT: A  936 CYS cc_start: 0.8560 (m) cc_final: 0.7945 (m)
REVERT: A  939 GLU cc_start: 0.7521 (tp30) cc_final: 0.6808 (tp30)
REVERT: A  940 PHE cc_start: 0.8542 (m-10) cc_final: 0.8268 (m-10)
REVERT: A 1021 CYS cc_start: 0.8238 (t) cc_final: 0.7998 (t)
REVERT: A 1023 THR cc_start: 0.7699 (m) cc_final: 0.7379 (m)
REVERT: A 1079 TYR cc_start: 0.6714 (m-10) cc_final: 0.6327 (m-10)
REVERT: A 1104 LEU cc_start: 0.6518 (mt) cc_final: 0.6133 (tp)
REVERT: A 1214 LYS cc_start: 0.8372 (mttt) cc_final: 0.7855 (pttm)
REVERT: A 1229 VAL cc_start: 0.8119 (t) cc_final: 0.7418 (t)
REVERT: A 1233 ASN cc_start: 0.7456 (m110) cc_final: 0.7033 (m-40)
REVERT: A 1320 GLN cc_start: 0.8226 (tp40) cc_final: 0.7616 (tp40)
REVERT: A 1324 ASP cc_start: 0.7909 (m-30) cc_final: 0.7499 (m-30)
REVERT: A 1332 VAL cc_start: 0.9149 (t) cc_final: 0.8797 (t)
REVERT: A 1346 LEU cc_start: 0.9064 (mt) cc_final: 0.8832 (mt)
REVERT: A 1357 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6555 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9090 (mttt) cc_final: 0.8649 (mttt)
REVERT: A 1371 VAL cc_start: 0.8894 (t) cc_final: 0.8685 (t)
REVERT: A 1384 LEU cc_start: 0.8594 (mt) cc_final: 0.8313 (mt)
REVERT: A 1392 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6464 (mm-30)
REVERT: A 1403 LEU cc_start: 0.8016 (mt) cc_final: 0.7686 (mp)
REVERT: A 1427 PHE cc_start: 0.5635 (m-80) cc_final: 0.5410 (m-10)
REVERT: A 1453 SER cc_start: 0.8400 (p) cc_final: 0.7869 (p)
REVERT: A 1456 GLU cc_start: 0.7545 (pp20) cc_final: 0.7199 (pp20)
REVERT: A 1467 LEU cc_start: 0.6584 (tp) cc_final: 0.6347 (tp)
REVERT: A 1488 ASP cc_start: 0.7304 (m-30) cc_final: 0.7061 (m-30)
REVERT: A 1502 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8184 (tp-100)
REVERT: A 1508 LEU cc_start: 0.8783 (tp) cc_final: 0.7303 (tp)
REVERT: A 1512 TYR cc_start: 0.7253 (m-10) cc_final: 0.6995 (m-80)
REVERT: A 1514 GLU cc_start: 0.7682 (mp0) cc_final: 0.6862 (mp0)
REVERT: A 1530 ASP cc_start: 0.6593 (m-30) cc_final: 0.6327 (m-30)
REVERT: A 1531 GLN cc_start: 0.8556 (mt0) cc_final: 0.7719 (mm110)
REVERT: A 1546 MET cc_start: 0.8707 (mtt) cc_final: 0.8399 (mtt)
REVERT: A 1598 GLN cc_start: 0.8300 (mt0) cc_final: 0.7989 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.2504
  time to fit residues: 101.2251
Evaluate side-chains
  266 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    0.3980
   chunk 120 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 228 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 GLN
A1490 GLN
A1502 GLN
A1633 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.5631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11310  Z= 0.254
  Angle     :  0.645   9.760  15262  Z= 0.337
  Chirality :  0.041   0.237   1709
  Planarity :  0.005   0.054   1973
  Dihedral  :  5.591  75.042   1510
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.83 (0.23), residues: 1375
  helix:  1.34 (0.18), residues: 783
  sheet: -0.81 (0.36), residues: 156
  loop : -0.20 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A 110 
 PHE   0.018   0.002   PHE A1260 
 TYR   0.015   0.002   TYR A1428 
 ARG   0.012   0.001   ARG A1454 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8245 (mm-30)
REVERT: A  164 LYS cc_start: 0.7579 (pptt) cc_final: 0.7375 (pptt)
REVERT: A  202 TYR cc_start: 0.7278 (m-10) cc_final: 0.6927 (m-10)
REVERT: A  230 MET cc_start: 0.7098 (mmp) cc_final: 0.6707 (mmp)
REVERT: A  257 ILE cc_start: 0.7542 (mt) cc_final: 0.6973 (mm)
REVERT: A  264 ASN cc_start: 0.7847 (t0) cc_final: 0.7550 (t0)
REVERT: A  430 ASP cc_start: 0.7646 (t0) cc_final: 0.7422 (m-30)
REVERT: A  539 TYR cc_start: 0.7431 (m-80) cc_final: 0.6754 (m-80)
REVERT: A  540 LYS cc_start: 0.8522 (mttp) cc_final: 0.8161 (pttm)
REVERT: A  577 MET cc_start: 0.5290 (ttt) cc_final: 0.4961 (ttp)
REVERT: A  598 ASP cc_start: 0.7941 (m-30) cc_final: 0.7172 (m-30)
REVERT: A  643 ASN cc_start: 0.8067 (m110) cc_final: 0.7766 (m110)
REVERT: A  691 SER cc_start: 0.7488 (m) cc_final: 0.7093 (p)
REVERT: A  721 PHE cc_start: 0.8572 (p90) cc_final: 0.8310 (p90)
REVERT: A  741 MET cc_start: 0.7779 (mtt) cc_final: 0.7171 (mtt)
REVERT: A  770 HIS cc_start: 0.8454 (m90) cc_final: 0.8231 (m90)
REVERT: A  792 HIS cc_start: 0.7673 (t-170) cc_final: 0.7301 (t70)
REVERT: A  859 TYR cc_start: 0.7600 (p90) cc_final: 0.7221 (p90)
REVERT: A  926 LYS cc_start: 0.8576 (mttt) cc_final: 0.8254 (mttt)
REVERT: A  928 GLU cc_start: 0.8647 (tt0) cc_final: 0.8394 (tt0)
REVERT: A  932 GLN cc_start: 0.8020 (mt0) cc_final: 0.7634 (tp40)
REVERT: A  936 CYS cc_start: 0.8560 (m) cc_final: 0.7903 (m)
REVERT: A  939 GLU cc_start: 0.7704 (tp30) cc_final: 0.7413 (tp30)
REVERT: A  977 MET cc_start: 0.7272 (ttm) cc_final: 0.6852 (mtm)
REVERT: A 1021 CYS cc_start: 0.8243 (t) cc_final: 0.7809 (t)
REVERT: A 1079 TYR cc_start: 0.6710 (m-10) cc_final: 0.6296 (m-10)
REVERT: A 1090 LEU cc_start: 0.7177 (tp) cc_final: 0.6931 (tp)
REVERT: A 1214 LYS cc_start: 0.8388 (mttt) cc_final: 0.7885 (pttm)
REVERT: A 1229 VAL cc_start: 0.8125 (t) cc_final: 0.7447 (t)
REVERT: A 1233 ASN cc_start: 0.7591 (m110) cc_final: 0.7168 (m-40)
REVERT: A 1250 HIS cc_start: 0.6577 (m90) cc_final: 0.5518 (m90)
REVERT: A 1290 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8494 (mmtm)
REVERT: A 1320 GLN cc_start: 0.8234 (tp40) cc_final: 0.7368 (tp-100)
REVERT: A 1324 ASP cc_start: 0.7962 (m-30) cc_final: 0.6945 (m-30)
REVERT: A 1332 VAL cc_start: 0.9168 (t) cc_final: 0.8827 (t)
REVERT: A 1346 LEU cc_start: 0.9103 (mt) cc_final: 0.8875 (mt)
REVERT: A 1357 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6536 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9014 (mttt) cc_final: 0.8791 (mttt)
REVERT: A 1371 VAL cc_start: 0.8882 (t) cc_final: 0.8659 (t)
REVERT: A 1403 LEU cc_start: 0.7997 (mt) cc_final: 0.7715 (mp)
REVERT: A 1427 PHE cc_start: 0.5851 (m-80) cc_final: 0.5608 (m-10)
REVERT: A 1453 SER cc_start: 0.8677 (p) cc_final: 0.8237 (p)
REVERT: A 1456 GLU cc_start: 0.7653 (pp20) cc_final: 0.7335 (pp20)
REVERT: A 1488 ASP cc_start: 0.7590 (m-30) cc_final: 0.7320 (m-30)
REVERT: A 1499 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7153 (mp0)
REVERT: A 1502 GLN cc_start: 0.8638 (tp40) cc_final: 0.8205 (tp-100)
REVERT: A 1514 GLU cc_start: 0.7617 (mp0) cc_final: 0.6970 (mp0)
REVERT: A 1530 ASP cc_start: 0.6623 (m-30) cc_final: 0.6367 (m-30)
REVERT: A 1531 GLN cc_start: 0.8590 (mt0) cc_final: 0.7750 (mm110)
REVERT: A 1537 ASN cc_start: 0.8528 (m110) cc_final: 0.8225 (m110)
REVERT: A 1542 LEU cc_start: 0.9203 (mt) cc_final: 0.8997 (mm)
REVERT: A 1619 ILE cc_start: 0.5346 (mt) cc_final: 0.5111 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 290
  average time/residue: 0.2425
  time to fit residues: 98.8228
Evaluate side-chains
  259 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 134 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 62 optimal weight:    0.1980
   chunk 11 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 ASN
A 591 GLN
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.5919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11310  Z= 0.206
  Angle     :  0.622   8.281  15262  Z= 0.324
  Chirality :  0.042   0.304   1709
  Planarity :  0.004   0.055   1973
  Dihedral  :  5.420  73.827   1510
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.95 (0.23), residues: 1375
  helix:  1.41 (0.18), residues: 785
  sheet: -0.85 (0.36), residues: 156
  loop : -0.08 (0.33), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP A 369 
 HIS   0.017   0.001   HIS A 256 
 PHE   0.014   0.002   PHE A1226 
 TYR   0.010   0.001   TYR A 730 
 ARG   0.006   0.001   ARG A 594 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 TYR cc_start: 0.7433 (m-10) cc_final: 0.7121 (m-10)
REVERT: A  258 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7814 (mm-30)
REVERT: A  264 ASN cc_start: 0.7722 (t0) cc_final: 0.7440 (t0)
REVERT: A  359 TRP cc_start: 0.5447 (p90) cc_final: 0.5233 (p90)
REVERT: A  362 HIS cc_start: 0.7343 (m90) cc_final: 0.7022 (m90)
REVERT: A  388 ILE cc_start: 0.8669 (pt) cc_final: 0.8276 (mm)
REVERT: A  419 MET cc_start: 0.7814 (mmp) cc_final: 0.7505 (mmp)
REVERT: A  430 ASP cc_start: 0.7604 (t0) cc_final: 0.7366 (m-30)
REVERT: A  440 LYS cc_start: 0.6509 (mmtt) cc_final: 0.6217 (tttp)
REVERT: A  519 CYS cc_start: 0.8645 (m) cc_final: 0.8433 (m)
REVERT: A  539 TYR cc_start: 0.7356 (m-80) cc_final: 0.6694 (m-80)
REVERT: A  540 LYS cc_start: 0.8432 (mttp) cc_final: 0.8122 (pttm)
REVERT: A  547 LYS cc_start: 0.6954 (tptt) cc_final: 0.6559 (tppt)
REVERT: A  577 MET cc_start: 0.5383 (ttt) cc_final: 0.5162 (ttp)
REVERT: A  591 GLN cc_start: 0.8302 (mp10) cc_final: 0.7807 (pm20)
REVERT: A  598 ASP cc_start: 0.7951 (m-30) cc_final: 0.7569 (m-30)
REVERT: A  691 SER cc_start: 0.7361 (m) cc_final: 0.6946 (p)
REVERT: A  741 MET cc_start: 0.7717 (mtt) cc_final: 0.7160 (mtt)
REVERT: A  768 LEU cc_start: 0.8641 (mt) cc_final: 0.8409 (mt)
REVERT: A  859 TYR cc_start: 0.7596 (p90) cc_final: 0.7233 (p90)
REVERT: A  926 LYS cc_start: 0.8421 (mttt) cc_final: 0.8203 (mttt)
REVERT: A  928 GLU cc_start: 0.8625 (tt0) cc_final: 0.8368 (tt0)
REVERT: A  932 GLN cc_start: 0.8009 (mt0) cc_final: 0.7594 (tp40)
REVERT: A  936 CYS cc_start: 0.8558 (m) cc_final: 0.7858 (m)
REVERT: A  939 GLU cc_start: 0.7653 (tp30) cc_final: 0.7357 (tp30)
REVERT: A  977 MET cc_start: 0.7383 (ttm) cc_final: 0.6603 (mtm)
REVERT: A 1079 TYR cc_start: 0.6765 (m-10) cc_final: 0.6321 (m-10)
REVERT: A 1090 LEU cc_start: 0.7379 (tp) cc_final: 0.6944 (tp)
REVERT: A 1214 LYS cc_start: 0.8343 (mttt) cc_final: 0.7844 (pttm)
REVERT: A 1224 HIS cc_start: 0.7563 (t-170) cc_final: 0.7360 (t-170)
REVERT: A 1229 VAL cc_start: 0.8091 (t) cc_final: 0.7391 (t)
REVERT: A 1233 ASN cc_start: 0.7758 (m110) cc_final: 0.7452 (m-40)
REVERT: A 1250 HIS cc_start: 0.6017 (m90) cc_final: 0.5472 (m90)
REVERT: A 1301 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7196 (mm-30)
REVERT: A 1320 GLN cc_start: 0.8167 (tp40) cc_final: 0.7765 (tp40)
REVERT: A 1324 ASP cc_start: 0.7929 (m-30) cc_final: 0.7623 (m-30)
REVERT: A 1332 VAL cc_start: 0.9139 (t) cc_final: 0.8845 (t)
REVERT: A 1357 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6542 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9131 (mttt) cc_final: 0.8805 (mttt)
REVERT: A 1377 LEU cc_start: 0.8519 (tp) cc_final: 0.8306 (tp)
REVERT: A 1382 SER cc_start: 0.8138 (t) cc_final: 0.7878 (t)
REVERT: A 1392 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6685 (mm-30)
REVERT: A 1403 LEU cc_start: 0.7793 (mt) cc_final: 0.7537 (mp)
REVERT: A 1453 SER cc_start: 0.8591 (p) cc_final: 0.8158 (p)
REVERT: A 1456 GLU cc_start: 0.7582 (pp20) cc_final: 0.7341 (pp20)
REVERT: A 1488 ASP cc_start: 0.7527 (m-30) cc_final: 0.7275 (m-30)
REVERT: A 1502 GLN cc_start: 0.8643 (tp40) cc_final: 0.8326 (tp-100)
REVERT: A 1512 TYR cc_start: 0.7368 (m-10) cc_final: 0.6950 (m-80)
REVERT: A 1530 ASP cc_start: 0.6598 (m-30) cc_final: 0.6348 (m-30)
REVERT: A 1531 GLN cc_start: 0.8522 (mt0) cc_final: 0.7679 (mm110)
REVERT: A 1537 ASN cc_start: 0.8492 (m110) cc_final: 0.8180 (m110)
REVERT: A 1542 LEU cc_start: 0.9171 (mt) cc_final: 0.8921 (mm)
REVERT: A 1546 MET cc_start: 0.8647 (mtt) cc_final: 0.8360 (mtt)
REVERT: A 1570 GLU cc_start: 0.7565 (mp0) cc_final: 0.7287 (mp0)
REVERT: A 1646 ARG cc_start: 0.7098 (ttt-90) cc_final: 0.6572 (ttt90)
  outliers start: 1
  outliers final: 0
  residues processed: 278
  average time/residue: 0.2579
  time to fit residues: 99.7941
Evaluate side-chains
  250 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 133 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 HIS
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1633 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
moved from start:          0.6208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11310  Z= 0.195
  Angle     :  0.621   8.050  15262  Z= 0.315
  Chirality :  0.041   0.286   1709
  Planarity :  0.004   0.053   1973
  Dihedral  :  5.242  71.332   1510
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  1.14 (0.23), residues: 1375
  helix:  1.59 (0.19), residues: 773
  sheet: -0.78 (0.36), residues: 156
  loop : -0.01 (0.33), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 369 
 HIS   0.004   0.001   HIS A 853 
 PHE   0.017   0.002   PHE A 370 
 TYR   0.011   0.001   TYR A1504 
 ARG   0.011   0.001   ARG A1454 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7880 (pt0)
REVERT: A  202 TYR cc_start: 0.7792 (m-10) cc_final: 0.7096 (m-10)
REVERT: A  241 LYS cc_start: 0.7817 (tptm) cc_final: 0.7389 (tppp)
REVERT: A  244 MET cc_start: 0.5905 (mmt) cc_final: 0.5640 (mmt)
REVERT: A  247 LEU cc_start: 0.7141 (mt) cc_final: 0.6885 (mt)
REVERT: A  419 MET cc_start: 0.7952 (mmp) cc_final: 0.7705 (mmp)
REVERT: A  430 ASP cc_start: 0.7702 (t0) cc_final: 0.7343 (m-30)
REVERT: A  440 LYS cc_start: 0.6604 (mmtt) cc_final: 0.6310 (tttp)
REVERT: A  539 TYR cc_start: 0.7374 (m-80) cc_final: 0.6749 (m-80)
REVERT: A  540 LYS cc_start: 0.8378 (mttp) cc_final: 0.8065 (pttm)
REVERT: A  577 MET cc_start: 0.5599 (ttt) cc_final: 0.5345 (ttp)
REVERT: A  591 GLN cc_start: 0.8283 (mp10) cc_final: 0.7782 (mp10)
REVERT: A  598 ASP cc_start: 0.7956 (m-30) cc_final: 0.7577 (m-30)
REVERT: A  691 SER cc_start: 0.7049 (m) cc_final: 0.6728 (p)
REVERT: A  722 GLN cc_start: 0.7105 (mt0) cc_final: 0.6452 (mt0)
REVERT: A  741 MET cc_start: 0.7681 (mtt) cc_final: 0.7165 (mtt)
REVERT: A  760 MET cc_start: 0.8023 (ttm) cc_final: 0.7704 (tpp)
REVERT: A  770 HIS cc_start: 0.8532 (m90) cc_final: 0.8167 (m90)
REVERT: A  859 TYR cc_start: 0.7700 (p90) cc_final: 0.7391 (p90)
REVERT: A  926 LYS cc_start: 0.8455 (mttt) cc_final: 0.8194 (mttt)
REVERT: A  928 GLU cc_start: 0.8620 (tt0) cc_final: 0.8351 (tt0)
REVERT: A  932 GLN cc_start: 0.8007 (mt0) cc_final: 0.7631 (tp40)
REVERT: A  936 CYS cc_start: 0.8533 (m) cc_final: 0.7892 (m)
REVERT: A  939 GLU cc_start: 0.7632 (tp30) cc_final: 0.7315 (tp30)
REVERT: A  953 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7577 (ttpp)
REVERT: A  977 MET cc_start: 0.7359 (ttm) cc_final: 0.6583 (mtm)
REVERT: A 1079 TYR cc_start: 0.6802 (m-10) cc_final: 0.6364 (m-10)
REVERT: A 1214 LYS cc_start: 0.8307 (mttt) cc_final: 0.7820 (pttm)
REVERT: A 1229 VAL cc_start: 0.8072 (t) cc_final: 0.7461 (t)
REVERT: A 1250 HIS cc_start: 0.5917 (m90) cc_final: 0.5467 (m90)
REVERT: A 1301 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7144 (mm-30)
REVERT: A 1320 GLN cc_start: 0.8113 (tp40) cc_final: 0.7421 (tp-100)
REVERT: A 1324 ASP cc_start: 0.7960 (m-30) cc_final: 0.6852 (m-30)
REVERT: A 1328 CYS cc_start: 0.8054 (m) cc_final: 0.7842 (m)
REVERT: A 1332 VAL cc_start: 0.9142 (t) cc_final: 0.8884 (t)
REVERT: A 1357 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6138 (tm-30)
REVERT: A 1361 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7738 (ptm-80)
REVERT: A 1377 LEU cc_start: 0.8487 (tp) cc_final: 0.8284 (tp)
REVERT: A 1403 LEU cc_start: 0.7741 (mt) cc_final: 0.7479 (mp)
REVERT: A 1453 SER cc_start: 0.8818 (p) cc_final: 0.8395 (p)
REVERT: A 1488 ASP cc_start: 0.7563 (m-30) cc_final: 0.7271 (m-30)
REVERT: A 1499 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7029 (mp0)
REVERT: A 1512 TYR cc_start: 0.7406 (m-10) cc_final: 0.7109 (m-80)
REVERT: A 1514 GLU cc_start: 0.7933 (mp0) cc_final: 0.7366 (mp0)
REVERT: A 1530 ASP cc_start: 0.6565 (m-30) cc_final: 0.6286 (m-30)
REVERT: A 1531 GLN cc_start: 0.8479 (mt0) cc_final: 0.7681 (mm110)
REVERT: A 1537 ASN cc_start: 0.8475 (m110) cc_final: 0.8223 (m110)
REVERT: A 1546 MET cc_start: 0.8557 (mtt) cc_final: 0.8175 (mmt)
REVERT: A 1619 ILE cc_start: 0.5507 (mt) cc_final: 0.5296 (mm)
REVERT: A 1646 ARG cc_start: 0.7122 (ttt-90) cc_final: 0.6778 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.2819
  time to fit residues: 109.1478
Evaluate side-chains
  244 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 121 optimal weight:    0.0030
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1233 ASN
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
A1381 GLN
A1425 ASN
A1502 GLN
A1633 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.6396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11310  Z= 0.186
  Angle     :  0.618   8.289  15262  Z= 0.315
  Chirality :  0.041   0.256   1709
  Planarity :  0.004   0.044   1973
  Dihedral  :  5.180  68.263   1510
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  1.21 (0.23), residues: 1375
  helix:  1.65 (0.19), residues: 770
  sheet: -0.79 (0.37), residues: 154
  loop :  0.06 (0.33), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 369 
 HIS   0.004   0.001   HIS A 853 
 PHE   0.018   0.002   PHE A 370 
 TYR   0.010   0.001   TYR A1504 
 ARG   0.007   0.001   ARG A1509 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7940 (pt0)
REVERT: A  202 TYR cc_start: 0.7447 (m-10) cc_final: 0.7157 (m-10)
REVERT: A  241 LYS cc_start: 0.7924 (tptm) cc_final: 0.7405 (tppp)
REVERT: A  244 MET cc_start: 0.6135 (mmt) cc_final: 0.5408 (mmt)
REVERT: A  257 ILE cc_start: 0.7327 (mt) cc_final: 0.7079 (mt)
REVERT: A  258 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7710 (mm-30)
REVERT: A  278 LEU cc_start: 0.8243 (mt) cc_final: 0.8026 (mt)
REVERT: A  370 PHE cc_start: 0.7341 (p90) cc_final: 0.7009 (p90)
REVERT: A  392 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7283 (mt-10)
REVERT: A  430 ASP cc_start: 0.7627 (t0) cc_final: 0.7163 (m-30)
REVERT: A  539 TYR cc_start: 0.7340 (m-80) cc_final: 0.6842 (m-80)
REVERT: A  540 LYS cc_start: 0.8344 (mttp) cc_final: 0.8051 (pttm)
REVERT: A  591 GLN cc_start: 0.8251 (mp10) cc_final: 0.7798 (mp10)
REVERT: A  598 ASP cc_start: 0.7906 (m-30) cc_final: 0.7428 (m-30)
REVERT: A  691 SER cc_start: 0.7131 (m) cc_final: 0.6856 (p)
REVERT: A  741 MET cc_start: 0.7744 (mtt) cc_final: 0.7213 (mtt)
REVERT: A  760 MET cc_start: 0.7971 (ttm) cc_final: 0.7696 (tpp)
REVERT: A  770 HIS cc_start: 0.8472 (m90) cc_final: 0.8158 (m90)
REVERT: A  859 TYR cc_start: 0.7728 (p90) cc_final: 0.7425 (p90)
REVERT: A  926 LYS cc_start: 0.8449 (mttt) cc_final: 0.8207 (mttt)
REVERT: A  928 GLU cc_start: 0.8621 (tt0) cc_final: 0.8370 (tt0)
REVERT: A  932 GLN cc_start: 0.8063 (mt0) cc_final: 0.7800 (tp40)
REVERT: A  936 CYS cc_start: 0.8653 (m) cc_final: 0.7815 (m)
REVERT: A  939 GLU cc_start: 0.7609 (tp30) cc_final: 0.7297 (tp30)
REVERT: A  953 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7599 (ttpp)
REVERT: A  977 MET cc_start: 0.7489 (ttm) cc_final: 0.6666 (mtm)
REVERT: A 1079 TYR cc_start: 0.6884 (m-10) cc_final: 0.6255 (m-10)
REVERT: A 1214 LYS cc_start: 0.8298 (mttt) cc_final: 0.7812 (pttm)
REVERT: A 1229 VAL cc_start: 0.8014 (t) cc_final: 0.7390 (t)
REVERT: A 1236 LEU cc_start: 0.8801 (mm) cc_final: 0.8595 (mm)
REVERT: A 1250 HIS cc_start: 0.5925 (m90) cc_final: 0.5494 (m90)
REVERT: A 1294 ASP cc_start: 0.8801 (m-30) cc_final: 0.8539 (m-30)
REVERT: A 1301 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7130 (mm-30)
REVERT: A 1319 LEU cc_start: 0.7650 (mt) cc_final: 0.7406 (mp)
REVERT: A 1320 GLN cc_start: 0.8116 (tp40) cc_final: 0.7437 (tp-100)
REVERT: A 1324 ASP cc_start: 0.8008 (m-30) cc_final: 0.7017 (m-30)
REVERT: A 1328 CYS cc_start: 0.8109 (m) cc_final: 0.7890 (m)
REVERT: A 1332 VAL cc_start: 0.9200 (t) cc_final: 0.8883 (t)
REVERT: A 1357 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6138 (tm-30)
REVERT: A 1361 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7464 (ptm160)
REVERT: A 1403 LEU cc_start: 0.7746 (mt) cc_final: 0.7473 (mp)
REVERT: A 1453 SER cc_start: 0.8772 (p) cc_final: 0.8359 (p)
REVERT: A 1488 ASP cc_start: 0.7642 (m-30) cc_final: 0.7405 (m-30)
REVERT: A 1512 TYR cc_start: 0.7416 (m-10) cc_final: 0.7065 (m-80)
REVERT: A 1530 ASP cc_start: 0.6535 (m-30) cc_final: 0.6179 (m-30)
REVERT: A 1531 GLN cc_start: 0.8439 (mt0) cc_final: 0.7666 (mm110)
REVERT: A 1537 ASN cc_start: 0.8447 (m110) cc_final: 0.8165 (m-40)
REVERT: A 1541 GLU cc_start: 0.8107 (tp30) cc_final: 0.7833 (tp30)
REVERT: A 1646 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6775 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2546
  time to fit residues: 95.5469
Evaluate side-chains
  242 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 128 optimal weight:    5.9990
   chunk 117 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 GLN
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
A1381 GLN
A1502 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.6619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11310  Z= 0.249
  Angle     :  0.677  10.974  15262  Z= 0.344
  Chirality :  0.042   0.266   1709
  Planarity :  0.004   0.043   1973
  Dihedral  :  5.248  65.420   1510
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.65 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.95 (0.23), residues: 1375
  helix:  1.43 (0.19), residues: 769
  sheet: -0.95 (0.37), residues: 163
  loop : -0.00 (0.33), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 369 
 HIS   0.006   0.001   HIS A  77 
 PHE   0.021   0.002   PHE A1260 
 TYR   0.012   0.002   TYR A 730 
 ARG   0.007   0.001   ARG A1454 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLU cc_start: 0.8543 (pt0) cc_final: 0.8275 (pm20)
REVERT: A  108 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7942 (pt0)
REVERT: A  202 TYR cc_start: 0.7640 (m-10) cc_final: 0.7318 (m-10)
REVERT: A  244 MET cc_start: 0.6307 (mmt) cc_final: 0.5812 (mmt)
REVERT: A  257 ILE cc_start: 0.7327 (mt) cc_final: 0.7080 (mt)
REVERT: A  258 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: A  278 LEU cc_start: 0.8253 (mt) cc_final: 0.7932 (mt)
REVERT: A  291 PHE cc_start: 0.5311 (m-80) cc_final: 0.5065 (m-80)
REVERT: A  370 PHE cc_start: 0.7415 (p90) cc_final: 0.7070 (p90)
REVERT: A  430 ASP cc_start: 0.7737 (t0) cc_final: 0.7241 (m-30)
REVERT: A  539 TYR cc_start: 0.7515 (m-80) cc_final: 0.7036 (m-80)
REVERT: A  540 LYS cc_start: 0.8494 (mttp) cc_final: 0.8185 (pttm)
REVERT: A  577 MET cc_start: 0.5531 (ttp) cc_final: 0.5074 (ttt)
REVERT: A  591 GLN cc_start: 0.8277 (mp10) cc_final: 0.7808 (mp10)
REVERT: A  598 ASP cc_start: 0.8207 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  691 SER cc_start: 0.7006 (m) cc_final: 0.6744 (p)
REVERT: A  741 MET cc_start: 0.7697 (mtt) cc_final: 0.7151 (mtt)
REVERT: A  760 MET cc_start: 0.7941 (ttm) cc_final: 0.7666 (tpp)
REVERT: A  859 TYR cc_start: 0.7799 (p90) cc_final: 0.7437 (p90)
REVERT: A  926 LYS cc_start: 0.8534 (mttt) cc_final: 0.8269 (mttt)
REVERT: A  928 GLU cc_start: 0.8635 (tt0) cc_final: 0.8368 (tt0)
REVERT: A  932 GLN cc_start: 0.8123 (mt0) cc_final: 0.7658 (tp40)
REVERT: A  936 CYS cc_start: 0.8572 (m) cc_final: 0.7789 (m)
REVERT: A  939 GLU cc_start: 0.7688 (tp30) cc_final: 0.7378 (tp30)
REVERT: A  953 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7437 (ttpp)
REVERT: A  977 MET cc_start: 0.7475 (ttm) cc_final: 0.6589 (mtm)
REVERT: A 1079 TYR cc_start: 0.6896 (m-10) cc_final: 0.6273 (m-10)
REVERT: A 1214 LYS cc_start: 0.8353 (mttt) cc_final: 0.7876 (pttm)
REVERT: A 1250 HIS cc_start: 0.6000 (m90) cc_final: 0.5531 (m90)
REVERT: A 1294 ASP cc_start: 0.8820 (m-30) cc_final: 0.8562 (m-30)
REVERT: A 1301 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7109 (mm-30)
REVERT: A 1319 LEU cc_start: 0.7785 (mt) cc_final: 0.7537 (mp)
REVERT: A 1320 GLN cc_start: 0.8050 (tp40) cc_final: 0.7694 (tp40)
REVERT: A 1324 ASP cc_start: 0.8270 (m-30) cc_final: 0.7859 (m-30)
REVERT: A 1328 CYS cc_start: 0.8218 (m) cc_final: 0.8006 (m)
REVERT: A 1332 VAL cc_start: 0.9210 (t) cc_final: 0.8898 (t)
REVERT: A 1357 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6239 (tm-30)
REVERT: A 1361 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7968 (ptm160)
REVERT: A 1366 LYS cc_start: 0.9120 (mttt) cc_final: 0.8411 (mttt)
REVERT: A 1369 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7390 (mp0)
REVERT: A 1377 LEU cc_start: 0.8635 (tp) cc_final: 0.8410 (tp)
REVERT: A 1403 LEU cc_start: 0.7719 (mt) cc_final: 0.7378 (mp)
REVERT: A 1488 ASP cc_start: 0.7660 (m-30) cc_final: 0.7363 (m-30)
REVERT: A 1530 ASP cc_start: 0.6599 (m-30) cc_final: 0.6323 (m-30)
REVERT: A 1531 GLN cc_start: 0.8510 (mt0) cc_final: 0.7651 (mm110)
REVERT: A 1537 ASN cc_start: 0.8482 (m110) cc_final: 0.8189 (m110)
REVERT: A 1541 GLU cc_start: 0.8119 (tp30) cc_final: 0.7823 (tp30)
REVERT: A 1546 MET cc_start: 0.8885 (mmt) cc_final: 0.8618 (mmm)
REVERT: A 1580 MET cc_start: 0.6174 (mtm) cc_final: 0.5818 (mtm)
REVERT: A 1619 ILE cc_start: 0.5580 (mt) cc_final: 0.5365 (mm)
REVERT: A 1646 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.6994 (ttt90)
  outliers start: 1
  outliers final: 1
  residues processed: 272
  average time/residue: 0.2477
  time to fit residues: 94.1706
Evaluate side-chains
  244 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 224 GLN
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 GLN
A1502 GLN
A1633 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11310  Z= 0.195
  Angle     :  0.640   8.347  15262  Z= 0.326
  Chirality :  0.041   0.249   1709
  Planarity :  0.004   0.057   1973
  Dihedral  :  5.115  62.114   1510
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.08 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  0.99 (0.23), residues: 1375
  helix:  1.46 (0.19), residues: 771
  sheet: -0.85 (0.37), residues: 163
  loop : -0.02 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 359 
 HIS   0.004   0.001   HIS A1224 
 PHE   0.021   0.002   PHE A 370 
 TYR   0.012   0.002   TYR A1505 
 ARG   0.006   0.001   ARG A 391 

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7928 (pt0)
REVERT: A  202 TYR cc_start: 0.7641 (m-10) cc_final: 0.7284 (m-10)
REVERT: A  221 PRO cc_start: 0.7892 (Cg_exo) cc_final: 0.7684 (Cg_endo)
REVERT: A  244 MET cc_start: 0.6188 (mmt) cc_final: 0.5711 (mmt)
REVERT: A  257 ILE cc_start: 0.7377 (mt) cc_final: 0.7142 (mt)
REVERT: A  258 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7814 (mm-30)
REVERT: A  278 LEU cc_start: 0.8208 (mt) cc_final: 0.7910 (mt)
REVERT: A  291 PHE cc_start: 0.5197 (m-80) cc_final: 0.4993 (m-80)
REVERT: A  359 TRP cc_start: 0.5263 (p90) cc_final: 0.4927 (p90)
REVERT: A  370 PHE cc_start: 0.7331 (p90) cc_final: 0.6980 (p90)
REVERT: A  392 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: A  430 ASP cc_start: 0.7662 (t0) cc_final: 0.7138 (m-30)
REVERT: A  487 ASN cc_start: 0.4244 (t0) cc_final: 0.3010 (p0)
REVERT: A  539 TYR cc_start: 0.7334 (m-80) cc_final: 0.6925 (m-80)
REVERT: A  540 LYS cc_start: 0.8380 (mttp) cc_final: 0.8094 (pttm)
REVERT: A  577 MET cc_start: 0.5946 (ttp) cc_final: 0.5499 (ttt)
REVERT: A  591 GLN cc_start: 0.8245 (mp10) cc_final: 0.7789 (mp10)
REVERT: A  598 ASP cc_start: 0.8156 (m-30) cc_final: 0.7761 (m-30)
REVERT: A  691 SER cc_start: 0.7037 (m) cc_final: 0.6751 (p)
REVERT: A  741 MET cc_start: 0.7643 (mtt) cc_final: 0.7098 (mtt)
REVERT: A  746 CYS cc_start: 0.7602 (m) cc_final: 0.7351 (m)
REVERT: A  760 MET cc_start: 0.7920 (ttm) cc_final: 0.7677 (tpp)
REVERT: A  859 TYR cc_start: 0.7766 (p90) cc_final: 0.7445 (p90)
REVERT: A  926 LYS cc_start: 0.8483 (mttt) cc_final: 0.8259 (mttt)
REVERT: A  928 GLU cc_start: 0.8608 (tt0) cc_final: 0.8343 (tt0)
REVERT: A  932 GLN cc_start: 0.8014 (mt0) cc_final: 0.7636 (tp40)
REVERT: A  936 CYS cc_start: 0.8541 (m) cc_final: 0.7765 (m)
REVERT: A  953 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7442 (ttpp)
REVERT: A  977 MET cc_start: 0.7506 (ttm) cc_final: 0.6656 (mtm)
REVERT: A 1079 TYR cc_start: 0.6881 (m-10) cc_final: 0.6264 (m-10)
REVERT: A 1214 LYS cc_start: 0.8319 (mttt) cc_final: 0.7837 (pttm)
REVERT: A 1229 VAL cc_start: 0.7970 (t) cc_final: 0.7538 (t)
REVERT: A 1233 ASN cc_start: 0.7593 (m110) cc_final: 0.7389 (m110)
REVERT: A 1250 HIS cc_start: 0.5985 (m90) cc_final: 0.5367 (m90)
REVERT: A 1294 ASP cc_start: 0.8854 (m-30) cc_final: 0.8589 (m-30)
REVERT: A 1301 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7099 (mm-30)
REVERT: A 1320 GLN cc_start: 0.7985 (tp40) cc_final: 0.7689 (tp40)
REVERT: A 1324 ASP cc_start: 0.8224 (m-30) cc_final: 0.7831 (m-30)
REVERT: A 1332 VAL cc_start: 0.9186 (t) cc_final: 0.8881 (t)
REVERT: A 1357 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6119 (tm-30)
REVERT: A 1361 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7443 (ptm160)
REVERT: A 1366 LYS cc_start: 0.9098 (mttt) cc_final: 0.8333 (mttt)
REVERT: A 1369 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7328 (mp0)
REVERT: A 1377 LEU cc_start: 0.8598 (tp) cc_final: 0.8395 (tp)
REVERT: A 1392 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6338 (mm-30)
REVERT: A 1403 LEU cc_start: 0.7674 (mt) cc_final: 0.7296 (mp)
REVERT: A 1453 SER cc_start: 0.8800 (p) cc_final: 0.8433 (p)
REVERT: A 1488 ASP cc_start: 0.7631 (m-30) cc_final: 0.7315 (m-30)
REVERT: A 1505 TYR cc_start: 0.7434 (t80) cc_final: 0.7063 (t80)
REVERT: A 1530 ASP cc_start: 0.6540 (m-30) cc_final: 0.6274 (m-30)
REVERT: A 1531 GLN cc_start: 0.8474 (mt0) cc_final: 0.7661 (mm110)
REVERT: A 1537 ASN cc_start: 0.8446 (m110) cc_final: 0.8164 (m110)
REVERT: A 1541 GLU cc_start: 0.8092 (tp30) cc_final: 0.7799 (tp30)
REVERT: A 1546 MET cc_start: 0.8861 (mmt) cc_final: 0.8547 (mmm)
REVERT: A 1619 ILE cc_start: 0.5562 (mt) cc_final: 0.5359 (mm)
REVERT: A 1646 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.6857 (ttt90)
  outliers start: 1
  outliers final: 1
  residues processed: 275
  average time/residue: 0.2669
  time to fit residues: 103.0740
Evaluate side-chains
  250 residues out of total 1223 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0980
   chunk 30 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1502 GLN
A1633 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.135427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.117008 restraints weight = 32888.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.120065 restraints weight = 21600.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.122235 restraints weight = 15420.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.6855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11310  Z= 0.185
  Angle     :  0.637   8.421  15262  Z= 0.324
  Chirality :  0.042   0.242   1709
  Planarity :  0.004   0.040   1973
  Dihedral  :  5.008  58.129   1510
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.33 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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:  1.06 (0.23), residues: 1375
  helix:  1.50 (0.19), residues: 771
  sheet: -0.68 (0.37), residues: 162
  loop : -0.02 (0.33), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 369 
 HIS   0.003   0.001   HIS A 916 
 PHE   0.022   0.002   PHE A 370 
 TYR   0.009   0.001   TYR A1504 
 ARG   0.006   0.000   ARG A 391 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2657.97 seconds
wall clock time: 48 minutes 47.24 seconds (2927.24 seconds total)