Starting phenix.real_space_refine (version: 1.21rc1)
on Fri Apr 21 12:20:12 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/04_2023/7whm_32504.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    6048      2.51       5
     N    1706      2.21       5
     O    1857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   45": "NH1" <-> "NH2"
    Residue "A ARG   47": "NH1" <-> "NH2"
    Residue "A GLU   54": "OE1" <-> "OE2"
    Residue "A ARG   57": "NH1" <-> "NH2"
    Residue "A ARG   62": "NH1" <-> "NH2"
    Residue "A GLU   89": "OE1" <-> "OE2"
    Residue "A GLU   91": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2"
    Residue "A ARG  166": "NH1" <-> "NH2"
    Residue "A ARG  198": "NH1" <-> "NH2"
    Residue "A ARG  219": "NH1" <-> "NH2"
    Residue "A ARG  247": "NH1" <-> "NH2"
    Residue "A ASP  257": "OD1" <-> "OD2"
    Residue "A ARG  277": "NH1" <-> "NH2"
    Residue "A ARG  280": "NH1" <-> "NH2"
    Residue "A ARG  312": "NH1" <-> "NH2"
    Residue "A GLU  339": "OE1" <-> "OE2"
    Residue "A GLU  348": "OE1" <-> "OE2"
    Residue "A ARG  353": "NH1" <-> "NH2"
    Residue "A ARG  382": "NH1" <-> "NH2"
    Residue "A ARG  386": "NH1" <-> "NH2"
    Residue "A ARG  437": "NH1" <-> "NH2"
    Residue "A ARG  467": "NH1" <-> "NH2"
    Residue "A PHE  468": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  471": "NH1" <-> "NH2"
    Residue "A ARG  518": "NH1" <-> "NH2"
    Residue "A ARG  521": "NH1" <-> "NH2"
    Residue "A ARG  524": "NH1" <-> "NH2"
    Residue "A ARG  551": "NH1" <-> "NH2"
    Residue "A ARG  563": "NH1" <-> "NH2"
    Residue "A ARG  575": "NH1" <-> "NH2"
    Residue "A ARG  645": "NH1" <-> "NH2"
    Residue "A GLU  667": "OE1" <-> "OE2"
    Residue "A TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  676": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  710": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  718": "OE1" <-> "OE2"
    Residue "A ARG  729": "NH1" <-> "NH2"
    Residue "A GLU  768": "OE1" <-> "OE2"
    Residue "A ASP  774": "OD1" <-> "OD2"
    Residue "A GLU  800": "OE1" <-> "OE2"
    Residue "A ARG  890": "NH1" <-> "NH2"
    Residue "A GLU  896": "OE1" <-> "OE2"
    Residue "A ARG  925": "NH1" <-> "NH2"
    Residue "A ARG  960": "NH1" <-> "NH2"
    Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1070": "OE1" <-> "OE2"
    Residue "A ARG 1080": "NH1" <-> "NH2"
    Residue "A ARG 1104": "NH1" <-> "NH2"
    Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1147": "NH1" <-> "NH2"
    Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1198": "NH1" <-> "NH2"
    Residue "A ARG 1212": "NH1" <-> "NH2"
    Residue "A ARG 1218": "NH1" <-> "NH2"
    Residue "A ARG 1220": "NH1" <-> "NH2"
    Residue "A ARG 1232": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 9650
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1214, 9650
          Classifications: {'peptide': 1214}
          Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1171}
  Time building chain proxies: 5.28, per 1000 atoms: 0.55
  Number of scatterers: 9650
  At special positions: 0
  Unit cell: (110.448, 128.502, 133.812, 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      39     16.00
     O    1857      8.00
     N    1706      7.00
     C    6048      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: 3.48
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2292

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      37.7% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 306 through 338
      removed outlier: 3.723A  pdb=" N   HIS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 372
      removed outlier: 3.534A  pdb=" N   ARG A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 631
      removed outlier: 3.562A  pdb=" N   ARG A 631 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 658
      removed outlier: 3.734A  pdb=" N   ASN A 655 " --> pdb=" O   MET A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 688
    Processing helix  chain 'A' and resid 718 through 724
    Processing helix  chain 'A' and resid 744 through 754
      removed outlier: 4.324A  pdb=" N   ARG A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 769
    Processing helix  chain 'A' and resid 773 through 777
    Processing helix  chain 'A' and resid 778 through 796
    Processing helix  chain 'A' and resid 800 through 814
      removed outlier: 3.739A  pdb=" N   ILE A 804 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 835
    Processing helix  chain 'A' and resid 835 through 850
    Processing helix  chain 'A' and resid 852 through 861
      removed outlier: 4.174A  pdb=" N   GLY A 861 " --> pdb=" O   THR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 885
    Processing helix  chain 'A' and resid 887 through 892
    Processing helix  chain 'A' and resid 897 through 901
    Processing helix  chain 'A' and resid 904 through 909
    Processing helix  chain 'A' and resid 909 through 923
    Processing helix  chain 'A' and resid 924 through 928
    Processing helix  chain 'A' and resid 932 through 937
    Processing helix  chain 'A' and resid 979 through 994
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing helix  chain 'A' and resid 1094 through 1105
    Processing helix  chain 'A' and resid 1123 through 1136
      removed outlier: 3.692A  pdb=" N   LEU A1133 " --> pdb=" O   MET A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1148 through 1161
      removed outlier: 4.027A  pdb=" N   PHE A1152 " --> pdb=" O   ASN A1148 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A1153 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1193
      removed outlier: 4.154A  pdb=" N   ALA A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1220
      removed outlier: 3.522A  pdb=" N   ARG A1220 " --> pdb=" O   LYS A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1236
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.934A  pdb=" N   ASN A 105 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   VAL A 235 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   GLN A 260 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   SER A 237 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   VAL A 258 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   HIS A 239 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   VAL A 256 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85
      removed outlier: 4.761A  pdb=" N   VAL A 296 " --> pdb=" O   LYS A1109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 181
      removed outlier: 6.390A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 149 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   TYR A 149 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   GLU A 157 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 139 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLN A 124 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ARG A 125 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 284 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   PHE A 127 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206
      removed outlier: 4.176A  pdb=" N   ASN A1053 " --> pdb=" O   ILE A1062 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE A1062 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A1063 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   ARG A1065 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 206
      removed outlier: 6.697A  pdb=" N   SER A1016 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 395
      removed outlier: 5.516A  pdb=" N   ARG A 382 " --> pdb=" O   ILE A 738 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ILE A 738 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   GLU A 384 " --> pdb=" O   ALA A 736 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ALA A 736 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ARG A 386 " --> pdb=" O   TRP A 734 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   TRP A 734 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ASP A 388 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   GLY A 732 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   THR A 725 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 725 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   VAL A 727 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   LEU A 568 " --> pdb=" O   VAL A 727 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 729 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU A 566 " --> pdb=" O   ARG A 729 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   HIS A 731 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   LEU A 564 " --> pdb=" O   HIS A 731 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASN A 733 " --> pdb=" O   GLY A 562 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLY A 562 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   SER A 735 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR A 560 " --> pdb=" O   SER A 735 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU A 573 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 409
      removed outlier: 6.814A  pdb=" N   GLN A 435 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   PHE A 676 " --> pdb=" O   GLN A 435 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ARG A 437 " --> pdb=" O   PHE A 676 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL A 678 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ILE A 439 " --> pdb=" O   VAL A 678 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   THR A 673 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLU A 667 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 458
      removed outlier: 5.587A  pdb=" N   ASN A 449 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN A 472 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   SER A 451 " --> pdb=" O   TYR A 470 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   TYR A 470 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   PHE A 453 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   PHE A 468 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASN A 455 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU A 466 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU A 545 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   SER A 469 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   VAL A 543 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ARG A 471 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   ILE A 541 " --> pdb=" O   ARG A 471 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 604 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 545 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ILE A 602 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   LEU A 547 " --> pdb=" O   CYS A 600 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   CYS A 600 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   GLY A 549 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU A 598 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY A 593 " --> pdb=" O   THR A 589 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 502
      removed outlier: 6.989A  pdb=" N   THR A 510 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 531
    Processing sheet with id=AB2, first strand: chain 'A' and resid 864 through 865
      removed outlier: 6.561A  pdb=" N   ASN A 864 " --> pdb=" O   GLU A1119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    462 hydrogen bonds defined for protein.
    1320 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: 3.70

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3261
        1.34 -     1.45: 1325
        1.45 -     1.57: 5168
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9828
  Sorted by residual:
  bond pdb=" CB  THR A1007 "
       pdb=" CG2 THR A1007 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.54e+00
  bond pdb=" CG1 ILE A1048 "
       pdb=" CD1 ILE A1048 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.29e+00
  bond pdb=" CA  GLY A 204 "
       pdb=" C   GLY A 204 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 1.39e-02 5.18e+03 2.09e+00
  bond pdb=" CB  ASP A 182 "
       pdb=" CG  ASP A 182 "
    ideal  model  delta    sigma   weight residual
    1.516  1.482  0.034 2.50e-02 1.60e+03 1.88e+00
  bond pdb=" CB  ASN A1148 "
       pdb=" CG  ASN A1148 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.74e+00
  ... (remaining 9823 not shown)

  Histogram of bond angle deviations from ideal:
       98.93 -   105.94: 165
      105.94 -   112.96: 5387
      112.96 -   119.98: 3216
      119.98 -   127.00: 4469
      127.00 -   134.02: 88
  Bond angle restraints: 13325
  Sorted by residual:
  angle pdb=" C   THR A 133 "
        pdb=" N   THR A 134 "
        pdb=" CA  THR A 134 "
      ideal   model   delta    sigma   weight residual
     122.74  129.54   -6.80 2.44e+00 1.68e-01 7.77e+00
  angle pdb=" C   TYR A 710 "
        pdb=" N   GLN A 711 "
        pdb=" CA  GLN A 711 "
      ideal   model   delta    sigma   weight residual
     122.61  126.39   -3.78 1.56e+00 4.11e-01 5.86e+00
  angle pdb=" N   LEU A 745 "
        pdb=" CA  LEU A 745 "
        pdb=" C   LEU A 745 "
      ideal   model   delta    sigma   weight residual
     109.81  115.13   -5.32 2.21e+00 2.05e-01 5.81e+00
  angle pdb=" CA  MET A 955 "
        pdb=" CB  MET A 955 "
        pdb=" CG  MET A 955 "
      ideal   model   delta    sigma   weight residual
     114.10  118.82   -4.72 2.00e+00 2.50e-01 5.57e+00
  angle pdb=" C   TYR A 615 "
        pdb=" N   LEU A 616 "
        pdb=" CA  LEU A 616 "
      ideal   model   delta    sigma   weight residual
     120.28  123.63   -3.35 1.44e+00 4.82e-01 5.42e+00
  ... (remaining 13320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5400
       17.65 -    35.30: 453
       35.30 -    52.96: 78
       52.96 -    70.61: 19
       70.61 -    88.26: 8
  Dihedral angle restraints: 5958
    sinusoidal: 2406
      harmonic: 3552
  Sorted by residual:
  dihedral pdb=" CA  ILE A 692 "
           pdb=" C   ILE A 692 "
           pdb=" N   SER A 693 "
           pdb=" CA  SER A 693 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  PRO A 700 "
           pdb=" C   PRO A 700 "
           pdb=" N   VAL A 701 "
           pdb=" CA  VAL A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.93  -22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  TYR A 706 "
           pdb=" C   TYR A 706 "
           pdb=" N   ALA A 707 "
           pdb=" CA  ALA A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.22  -17.78     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 969
       0.040 -    0.081: 378
       0.081 -    0.121: 150
       0.121 -    0.161: 18
       0.161 -    0.202: 2
  Chirality restraints: 1517
  Sorted by residual:
  chirality pdb=" CB  VAL A 904 "
            pdb=" CA  VAL A 904 "
            pdb=" CG1 VAL A 904 "
            pdb=" CG2 VAL A 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  THR A1007 "
            pdb=" CA  THR A1007 "
            pdb=" OG1 THR A1007 "
            pdb=" CG2 THR A1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  VAL A 113 "
            pdb=" N   VAL A 113 "
            pdb=" C   VAL A 113 "
            pdb=" CB  VAL A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  ... (remaining 1514 not shown)

  Planarity restraints: 1737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 134 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 135 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 135 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 135 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 398 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A 399 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 399 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 399 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 149 "   -0.009 2.00e-02 2.50e+03   9.94e-03 1.98e+00
        pdb=" CG  TYR A 149 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 149 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 149 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 149 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 149 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 149 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 149 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1734 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 240
        2.70 -     3.25: 9086
        3.25 -     3.80: 15015
        3.80 -     4.35: 19729
        4.35 -     4.90: 33490
  Nonbonded interactions: 77560
  Sorted by model distance:
  nonbonded pdb=" O   THR A  84 "
            pdb=" NH1 ARG A 960 "
     model   vdw
     2.155 2.520
  nonbonded pdb=" O   LEU A 482 "
            pdb=" NE2 GLN A 531 "
     model   vdw
     2.222 2.520
  nonbonded pdb=" OH  TYR A 470 "
            pdb=" OE1 GLN A 472 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OD1 ASP A 309 "
            pdb=" NH2 ARG A 312 "
     model   vdw
     2.262 2.520
  nonbonded pdb=" O   TYR A  72 "
            pdb=" OG1 THR A  75 "
     model   vdw
     2.313 2.440
  ... (remaining 77555 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.790
  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:          7.900
  Check model and map are aligned:         0.130
  Set scattering table:                    0.100
  Process input model:                     27.840
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9828  Z= 0.414
  Angle     :  0.637   6.811  13325  Z= 0.364
  Chirality :  0.048   0.202   1517
  Planarity :  0.004   0.040   1737
  Dihedral  : 13.847  88.259   3666
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.15 (0.23), residues: 1212
  helix:  1.29 (0.25), residues: 416
  sheet:  0.04 (0.29), residues: 292
  loop : -0.82 (0.25), residues: 504

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.182 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 155
  average time/residue: 1.5459
  time to fit residues: 253.9850
Evaluate side-chains
  137 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.040 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 1.0524
  time to fit residues: 2.6042
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 109 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 260 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.0835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9828  Z= 0.239
  Angle     :  0.537   7.089  13325  Z= 0.290
  Chirality :  0.045   0.160   1517
  Planarity :  0.004   0.042   1737
  Dihedral  :  4.749  24.951   1349
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer Outliers :  2.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.74 (0.24), residues: 1212
  helix:  2.06 (0.25), residues: 406
  sheet:  0.33 (0.30), residues: 277
  loop : -0.64 (0.25), residues: 529

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 1.115 
Fit side-chains
  outliers start: 27
  outliers final: 8
  residues processed: 151
  average time/residue: 1.5299
  time to fit residues: 245.1649
Evaluate side-chains
  151 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 1.174 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 3
  residues processed: 5
  average time/residue: 0.0953
  time to fit residues: 2.3444
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 109 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9828  Z= 0.179
  Angle     :  0.484   5.655  13325  Z= 0.262
  Chirality :  0.043   0.155   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.472  22.645   1349
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer Outliers :  2.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 (0.24), residues: 1212
  helix:  2.37 (0.26), residues: 406
  sheet:  0.55 (0.30), residues: 276
  loop : -0.53 (0.26), residues: 530

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.406 
Fit side-chains
  outliers start: 24
  outliers final: 10
  residues processed: 153
  average time/residue: 1.3949
  time to fit residues: 227.4968
Evaluate side-chains
  152 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 1.148 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 4
  residues processed: 6
  average time/residue: 0.1194
  time to fit residues: 2.7968
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9828  Z= 0.164
  Angle     :  0.473   5.671  13325  Z= 0.255
  Chirality :  0.043   0.154   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.325  21.447   1349
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer Outliers :  2.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.24 (0.24), residues: 1212
  helix:  2.55 (0.26), residues: 406
  sheet:  0.62 (0.30), residues: 281
  loop : -0.43 (0.27), residues: 525

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 1.212 
Fit side-chains
  outliers start: 28
  outliers final: 10
  residues processed: 153
  average time/residue: 1.4643
  time to fit residues: 239.3506
Evaluate side-chains
  151 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.115 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 4
  residues processed: 6
  average time/residue: 0.2972
  time to fit residues: 3.8939
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0070
   chunk 48 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.7202

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9828  Z= 0.262
  Angle     :  0.519   7.016  13325  Z= 0.279
  Chirality :  0.045   0.161   1517
  Planarity :  0.004   0.045   1737
  Dihedral  :  4.464  21.180   1349
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer Outliers :  2.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 (0.24), residues: 1212
  helix:  2.38 (0.25), residues: 406
  sheet:  0.61 (0.30), residues: 281
  loop : -0.44 (0.26), residues: 525

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 1.232 
Fit side-chains
  outliers start: 27
  outliers final: 14
  residues processed: 152
  average time/residue: 1.4684
  time to fit residues: 237.6868
Evaluate side-chains
  154 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.187 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 5
  residues processed: 9
  average time/residue: 0.5367
  time to fit residues: 7.1038
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 117 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
A 754 HIS
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9828  Z= 0.195
  Angle     :  0.484   6.273  13325  Z= 0.261
  Chirality :  0.043   0.156   1517
  Planarity :  0.003   0.042   1737
  Dihedral  :  4.361  20.510   1349
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer Outliers :  2.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.26 (0.24), residues: 1212
  helix:  2.53 (0.25), residues: 406
  sheet:  0.69 (0.31), residues: 277
  loop : -0.42 (0.26), residues: 529

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.126 
Fit side-chains
  outliers start: 27
  outliers final: 8
  residues processed: 151
  average time/residue: 1.4343
  time to fit residues: 230.8871
Evaluate side-chains
  147 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 1.183 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 4
  residues processed: 4
  average time/residue: 0.4231
  time to fit residues: 3.6713
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0370
   overall best weight:    1.5262

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
A 754 HIS
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9828  Z= 0.236
  Angle     :  0.509   6.814  13325  Z= 0.273
  Chirality :  0.044   0.160   1517
  Planarity :  0.004   0.042   1737
  Dihedral  :  4.416  20.241   1349
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer Outliers :  2.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.23 (0.24), residues: 1212
  helix:  2.44 (0.25), residues: 406
  sheet:  0.69 (0.31), residues: 278
  loop : -0.40 (0.26), residues: 528

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 1.065 
Fit side-chains
  outliers start: 24
  outliers final: 12
  residues processed: 151
  average time/residue: 1.4102
  time to fit residues: 226.7944
Evaluate side-chains
  153 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 1.133 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 4
  residues processed: 8
  average time/residue: 0.3624
  time to fit residues: 5.1259
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 101 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9828  Z= 0.340
  Angle     :  0.560   8.225  13325  Z= 0.300
  Chirality :  0.046   0.164   1517
  Planarity :  0.004   0.060   1737
  Dihedral  :  4.617  21.244   1349
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer Outliers :  1.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.08 (0.24), residues: 1212
  helix:  2.23 (0.25), residues: 406
  sheet:  0.61 (0.30), residues: 281
  loop : -0.41 (0.26), residues: 525

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 1.140 
Fit side-chains
  outliers start: 17
  outliers final: 10
  residues processed: 148
  average time/residue: 1.4556
  time to fit residues: 230.0870
Evaluate side-chains
  151 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.173 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 5
  average time/residue: 0.4171
  time to fit residues: 3.9512
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 108 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 114 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9828  Z= 0.156
  Angle     :  0.468   5.749  13325  Z= 0.252
  Chirality :  0.042   0.154   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.303  20.471   1349
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer Outliers :  0.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.35 (0.24), residues: 1212
  helix:  2.62 (0.25), residues: 404
  sheet:  0.68 (0.31), residues: 281
  loop : -0.34 (0.27), residues: 527

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 1.046 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 145
  average time/residue: 1.6133
  time to fit residues: 249.9949
Evaluate side-chains
  141 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 1.224 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 1.7246
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0040
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 102 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 260 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN
A1139 GLN
** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9828  Z= 0.123
  Angle     :  0.440   5.059  13325  Z= 0.237
  Chirality :  0.042   0.148   1517
  Planarity :  0.003   0.040   1737
  Dihedral  :  4.081  18.193   1349
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer Outliers :  0.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.48 (0.24), residues: 1212
  helix:  2.82 (0.25), residues: 405
  sheet:  0.73 (0.30), residues: 283
  loop : -0.34 (0.27), residues: 524

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 1.109 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 156
  average time/residue: 1.4137
  time to fit residues: 235.1173
Evaluate side-chains
  147 residues out of total 1077 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 1.156 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 3
  residues processed: 3
  average time/residue: 0.1194
  time to fit residues: 2.2175
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 98 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 69 optimal weight:    9.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.142372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.095892 restraints weight = 11082.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 1.58
r_work: 0.2790 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9828  Z= 0.177
  Angle     :  0.477   6.015  13325  Z= 0.256
  Chirality :  0.043   0.155   1517
  Planarity :  0.003   0.042   1737
  Dihedral  :  4.154  18.054   1349
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer Outliers :  0.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  1.45 (0.24), residues: 1212
  helix:  2.68 (0.25), residues: 405
  sheet:  0.76 (0.30), residues: 283
  loop : -0.28 (0.27), residues: 524

===============================================================================
Job complete
usr+sys time: 4310.86 seconds
wall clock time: 76 minutes 47.66 seconds (4607.66 seconds total)