Starting phenix.real_space_refine
on Fri Dec  8 10:28:30 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/12_2023/7wit_32535_updated.pdb"
  }
  resolution = 3.21
  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=   0.007 sd=   0.105
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      38      5.16       5
     C    5222      2.51       5
     N    1396      2.21       5
     O    1450      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  536": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  738": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  794": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  799": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8109
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1135, 8109
          Unusual residues: {'9I0': 1, 'ATP': 1}
          Classifications: {'peptide': 1133, 'undetermined': 2}
          Incomplete info: {'truncation_to_alanine': 239}
          Link IDs: {'PTRANS': 35, 'TRANS': 1097, None: 2}
            Not linked:
              pdbres="ARG A1579 "
              pdbres="ATP A2001 "
            Not linked:
              pdbres="ATP A2001 "
              pdbres="9I0 A2002 "
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 860
          Unresolved non-hydrogen angles: 1072
          Unresolved non-hydrogen dihedrals: 686
          Unresolved non-hydrogen chiralities: 81
          Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 468
  Time building chain proxies: 5.04, per 1000 atoms: 0.62
  Number of scatterers: 8109
  At special positions: 0
  Unit cell: (97.185, 133.76, 77.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       3     15.00
     O    1450      8.00
     N    1396      7.00
     C    5222      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: 3.07
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      63.6% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 231 through 242
      removed outlier: 4.075A  pdb=" N   ALA A 235 " --> pdb=" O   TRP A 232 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS A 241 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 274
    Processing helix  chain 'A' and resid 284 through 294
      removed outlier: 3.592A  pdb=" N   TRP A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 328
      removed outlier: 3.679A  pdb=" N   LEU A 301 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER A 302 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   GLY A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      Proline residue:  A 317  - end of helix
    Processing helix  chain 'A' and resid 355 through 399
      removed outlier: 3.876A  pdb=" N   THR A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLN A 374 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
      removed outlier: 3.940A  pdb=" N   CYS A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 433
    Processing helix  chain 'A' and resid 436 through 456
      removed outlier: 5.087A  pdb=" N   MET A 441 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
      removed outlier: 3.792A  pdb=" N   ILE A 445 " --> pdb=" O   PRO A 442 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE A 446 " --> pdb=" O   VAL A 443 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A 447 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A 456 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 504
      removed outlier: 3.576A  pdb=" N   ILE A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE A 467 " --> pdb=" O   GLY A 463 " (cutoff:3.500A)
      Proline residue:  A 472  - end of helix
      removed outlier: 3.874A  pdb=" N   HIS A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 512
    Processing helix  chain 'A' and resid 515 through 564
      removed outlier: 3.927A  pdb=" N   ALA A 535 " --> pdb=" O   THR A 531 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE A 536 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER A 543 " --> pdb=" O   TYR A 539 " (cutoff:3.500A)
      Proline residue:  A 551  - end of helix
    Processing helix  chain 'A' and resid 573 through 613
      removed outlier: 3.681A  pdb=" N   ILE A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   THR A 588 " --> pdb=" O   HIS A 584 " (cutoff:3.500A)
      Proline residue:  A 589  - end of helix
      removed outlier: 4.865A  pdb=" N   SER A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   SER A 595 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 605 " --> pdb=" O   VAL A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 726
    Processing helix  chain 'A' and resid 784 through 789
    Processing helix  chain 'A' and resid 796 through 806
    Processing helix  chain 'A' and resid 809 through 814
      removed outlier: 3.737A  pdb=" N   ILE A 814 " --> pdb=" O   PRO A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 827
      No H-bonds generated for 'chain 'A' and resid 825 through 827'
    Processing helix  chain 'A' and resid 832 through 845
      removed outlier: 3.516A  pdb=" N   ARG A 837 " --> pdb=" O   GLY A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 871
    Processing helix  chain 'A' and resid 891 through 893
      No H-bonds generated for 'chain 'A' and resid 891 through 893'
    Processing helix  chain 'A' and resid 914 through 920
    Processing helix  chain 'A' and resid 998 through 1006
    Processing helix  chain 'A' and resid 1010 through 1024
    Processing helix  chain 'A' and resid 1027 through 1038
      removed outlier: 3.941A  pdb=" N   ASP A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1062 through 1105
      removed outlier: 4.047A  pdb=" N   VAL A1086 " --> pdb=" O   THR A1082 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU A1087 " --> pdb=" O   SER A1083 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS A1098 " --> pdb=" O   ALA A1094 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A1104 " --> pdb=" O   SER A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1110 through 1115
    Processing helix  chain 'A' and resid 1118 through 1126
      removed outlier: 3.906A  pdb=" N   ARG A1124 " --> pdb=" O   SER A1120 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE A1125 " --> pdb=" O   ILE A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1128 through 1134
    Processing helix  chain 'A' and resid 1136 through 1160
      removed outlier: 3.554A  pdb=" N   SER A1158 " --> pdb=" O   LEU A1154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1209
      removed outlier: 3.890A  pdb=" N   LEU A1169 " --> pdb=" O   VAL A1166 " (cutoff:3.500A)
      Proline residue:  A1170  - end of helix
      removed outlier: 4.366A  pdb=" N   VAL A1174 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS A1175 " --> pdb=" O   ALA A1172 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE A1178 " --> pdb=" O   CYS A1175 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR A1181 " --> pdb=" O   ILE A1178 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL A1184 " --> pdb=" O   TYR A1181 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   SER A1186 " --> pdb=" O   ARG A1183 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG A1187 " --> pdb=" O   VAL A1184 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN A1190 " --> pdb=" O   ARG A1187 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP A1193 " --> pdb=" O   GLN A1190 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A1195 " --> pdb=" O   LEU A1192 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR A1196 " --> pdb=" O   ASP A1193 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU A1198 " --> pdb=" O   THR A1195 " (cutoff:3.500A)
      Proline residue:  A1199  - end of helix
      removed outlier: 3.553A  pdb=" N   SER A1202 " --> pdb=" O   PRO A1199 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU A1209 " --> pdb=" O   GLU A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1211 through 1216
    Processing helix  chain 'A' and resid 1220 through 1273
      removed outlier: 3.536A  pdb=" N   LEU A1228 " --> pdb=" O   GLN A1224 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A1229 " --> pdb=" O   GLN A1225 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A1237 " --> pdb=" O   SER A1233 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A1241 " --> pdb=" O   ALA A1237 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR A1242 " --> pdb=" O   SER A1238 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA A1243 " --> pdb=" O   LEU A1239 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A1261 " --> pdb=" O   ALA A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1288
      removed outlier: 3.577A  pdb=" N   TYR A1287 " --> pdb=" O   LEU A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1320
      removed outlier: 3.820A  pdb=" N   GLY A1310 " --> pdb=" O   GLU A1306 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ALA A1311 " --> pdb=" O   ILE A1307 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL A1312 " --> pdb=" O   GLN A1308 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A1320 " --> pdb=" O   HIS A1316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1385 through 1393
      removed outlier: 3.840A  pdb=" N   SER A1389 " --> pdb=" O   LYS A1385 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU A1390 " --> pdb=" O   SER A1386 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE A1392 " --> pdb=" O   PHE A1388 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   PHE A1393 " --> pdb=" O   SER A1389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1415 through 1421
      removed outlier: 4.062A  pdb=" N   SER A1420 " --> pdb=" O   HIS A1416 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ARG A1421 " --> pdb=" O   THR A1417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1437 through 1440
      No H-bonds generated for 'chain 'A' and resid 1437 through 1440'
    Processing helix  chain 'A' and resid 1448 through 1457
    Processing helix  chain 'A' and resid 1461 through 1466
    Processing helix  chain 'A' and resid 1484 through 1498
      removed outlier: 3.780A  pdb=" N   ARG A1498 " --> pdb=" O   ARG A1494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1514 through 1526
    Processing helix  chain 'A' and resid 1563 through 1569
      removed outlier: 3.738A  pdb=" N   SER A1568 " --> pdb=" O   GLU A1564 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 680 through 682
    Processing sheet with id=  B, first strand: chain 'A' and resid 709 through 713
      removed outlier: 6.850A  pdb=" N   TRP A 899 " --> pdb=" O   MET A 710 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL A 712 " --> pdb=" O   TRP A 899 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE A 901 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ARG A 910 " --> pdb=" O   ALA A 902 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS A 904 " --> pdb=" O   ILE A 908 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   ILE A 908 " --> pdb=" O   LYS A 904 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 770 through 773
      removed outlier: 7.098A  pdb=" N   VAL A 850 " --> pdb=" O   ALA A 771 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   ALA A 773 " --> pdb=" O   VAL A 850 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE A 852 " --> pdb=" O   ALA A 773 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   THR A 883 " --> pdb=" O   VAL A 851 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 853 " --> pdb=" O   THR A 883 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL A 885 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'A' and resid 1367 through 1369
      removed outlier: 3.808A  pdb=" N   ALA A1367 " --> pdb=" O   ILE A1347 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 1548 through 1552
      removed outlier: 6.700A  pdb=" N   PHE A1503 " --> pdb=" O   VAL A1534 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ILE A1536 " --> pdb=" O   PHE A1503 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   MET A1505 " --> pdb=" O   ILE A1536 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 685 through 687
      removed outlier: 3.515A  pdb=" N   SER A 734 " --> pdb=" O   PHE A 685 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   THR A 687 " --> pdb=" O   LYS A 732 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LYS A 732 " --> pdb=" O   THR A 687 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2156
        1.33 -     1.45: 1353
        1.45 -     1.57: 4689
        1.57 -     1.69: 5
        1.69 -     1.81: 59
  Bond restraints: 8262
  Sorted by residual:
  bond pdb=" C12 9I0 A2002 "
       pdb=" O1  9I0 A2002 "
    ideal  model  delta    sigma   weight residual
    1.250  1.328 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" C10 9I0 A2002 "
       pdb=" C12 9I0 A2002 "
    ideal  model  delta    sigma   weight residual
    1.545  1.493  0.052 2.00e-02 2.50e+03 6.69e+00
  bond pdb=" C12 9I0 A2002 "
       pdb=" O2  9I0 A2002 "
    ideal  model  delta    sigma   weight residual
    1.246  1.218  0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C   9I0 A2002 "
       pdb=" C1  9I0 A2002 "
    ideal  model  delta    sigma   weight residual
    1.541  1.515  0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" N   9I0 A2002 "
       pdb=" C8  9I0 A2002 "
    ideal  model  delta    sigma   weight residual
    1.346  1.321  0.025 2.00e-02 2.50e+03 1.52e+00
  ... (remaining 8257 not shown)

  Histogram of bond angle deviations from ideal:
       99.89 -   107.86: 286
      107.86 -   115.84: 5151
      115.84 -   123.82: 5683
      123.82 -   131.79: 158
      131.79 -   139.77: 20
  Bond angle restraints: 11298
  Sorted by residual:
  angle pdb=" N   VAL A1028 "
        pdb=" CA  VAL A1028 "
        pdb=" C   VAL A1028 "
      ideal   model   delta    sigma   weight residual
     111.81  108.62    3.19 8.60e-01 1.35e+00 1.38e+01
  angle pdb=" N   LYS A1445 "
        pdb=" CA  LYS A1445 "
        pdb=" C   LYS A1445 "
      ideal   model   delta    sigma   weight residual
     114.31  110.43    3.88 1.29e+00 6.01e-01 9.04e+00
  angle pdb=" O1  9I0 A2002 "
        pdb=" C12 9I0 A2002 "
        pdb=" O2  9I0 A2002 "
      ideal   model   delta    sigma   weight residual
     126.72  119.32    7.40 3.00e+00 1.11e-01 6.08e+00
  angle pdb=" C   ILE A1105 "
        pdb=" CA  ILE A1105 "
        pdb=" CB  ILE A1105 "
      ideal   model   delta    sigma   weight residual
     112.26  108.76    3.50 1.62e+00 3.81e-01 4.67e+00
  angle pdb=" N   MET A1025 "
        pdb=" CA  MET A1025 "
        pdb=" C   MET A1025 "
      ideal   model   delta    sigma   weight residual
     113.28  110.68    2.60 1.22e+00 6.72e-01 4.53e+00
  ... (remaining 11293 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.66: 4412
       12.66 -    25.31: 349
       25.31 -    37.97: 94
       37.97 -    50.62: 32
       50.62 -    63.28: 13
  Dihedral angle restraints: 4900
    sinusoidal: 1602
      harmonic: 3298
  Sorted by residual:
  dihedral pdb=" CA  TYR A 539 "
           pdb=" C   TYR A 539 "
           pdb=" N   THR A 540 "
           pdb=" CA  THR A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  HIS A1024 "
           pdb=" C   HIS A1024 "
           pdb=" N   MET A1025 "
           pdb=" CA  MET A1025 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.57   17.43     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ARG A 370 "
           pdb=" C   ARG A 370 "
           pdb=" N   THR A 371 "
           pdb=" CA  THR A 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 791
       0.030 -    0.059: 450
       0.059 -    0.089: 96
       0.089 -    0.119: 58
       0.119 -    0.148: 6
  Chirality restraints: 1401
  Sorted by residual:
  chirality pdb=" CA  GLN A 219 "
            pdb=" N   GLN A 219 "
            pdb=" C   GLN A 219 "
            pdb=" CB  GLN A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  ARG A1531 "
            pdb=" N   ARG A1531 "
            pdb=" C   ARG A1531 "
            pdb=" CB  ARG A1531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  THR A 588 "
            pdb=" N   THR A 588 "
            pdb=" C   THR A 588 "
            pdb=" CB  THR A 588 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 1398 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   9I0 A2002 "   -0.001 2.00e-02 2.50e+03   5.61e-02 4.73e+01
        pdb=" O   9I0 A2002 "    0.069 2.00e-02 2.50e+03
        pdb=" C2  9I0 A2002 "   -0.068 2.00e-02 2.50e+03
        pdb=" C3  9I0 A2002 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  9I0 A2002 "    0.005 2.00e-02 2.50e+03
        pdb=" C9  9I0 A2002 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 316 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO A 317 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 588 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.35e+00
        pdb=" N   PRO A 589 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2149
        2.80 -     3.32: 8284
        3.32 -     3.85: 12685
        3.85 -     4.37: 14972
        4.37 -     4.90: 25539
  Nonbonded interactions: 63629
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 554 "
            pdb=" OG1 THR A 558 "
     model   vdw
     2.271 2.440
  nonbonded pdb=" O   THR A1161 "
            pdb=" OG1 THR A1161 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" O   ASP A 424 "
            pdb=" OG  SER A 606 "
     model   vdw
     2.299 2.440
  nonbonded pdb=" O   ASP A 861 "
            pdb=" OG  SER A 865 "
     model   vdw
     2.328 2.440
  nonbonded pdb=" OD2 ASP A1031 "
            pdb=" OH  TYR A1287 "
     model   vdw
     2.330 2.440
  ... (remaining 63624 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  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:          3.950
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     26.950
  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:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
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      :  0.005   0.078   8262  Z= 0.314
  Angle     :  0.565   7.398  11298  Z= 0.299
  Chirality :  0.040   0.148   1401
  Planarity :  0.004   0.056   1407
  Dihedral  : 11.490  63.276   2754
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  :  7.04 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.25), residues: 1115
  helix: -0.59 (0.18), residues: 750
  sheet: -0.30 (0.70), residues: 68
  loop : -0.19 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 739 
   HIS   0.002   0.001   HIS A 293 
   PHE   0.010   0.001   PHE A1217 
   TYR   0.011   0.001   TYR A 230 
   ARG   0.002   0.000   ARG A1314 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 4
  residues processed: 150
  average time/residue: 0.2259
  time to fit residues: 44.9419
Evaluate side-chains
  89 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.913 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0733
  time to fit residues: 1.7722
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.0040
   chunk 85 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 102 optimal weight:    0.1980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 836 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8262  Z= 0.153
  Angle     :  0.511   8.664  11298  Z= 0.263
  Chirality :  0.039   0.161   1401
  Planarity :  0.004   0.033   1407
  Dihedral  :  6.526  63.387   1258
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.18 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1115
  helix:  0.85 (0.19), residues: 762
  sheet: -0.20 (0.72), residues: 63
  loop : -0.32 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A1033 
   HIS   0.003   0.001   HIS A1098 
   PHE   0.026   0.001   PHE A 738 
   TYR   0.013   0.001   TYR A 845 
   ARG   0.006   0.001   ARG A 835 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1733
  time to fit residues: 25.8886
Evaluate side-chains
  81 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.928 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0773
  time to fit residues: 1.6810
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 102 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   chunk 91 optimal weight:    0.0060
   chunk 101 optimal weight:    0.0470
   chunk 35 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.5294

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

Flipped N/Q/H residues before XYZ refinement:
A1296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   8262  Z= 0.142
  Angle     :  0.474   6.616  11298  Z= 0.239
  Chirality :  0.038   0.142   1401
  Planarity :  0.003   0.033   1407
  Dihedral  :  5.962  64.268   1258
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.29 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1115
  helix:  1.30 (0.19), residues: 759
  sheet: -0.02 (0.70), residues: 69
  loop : -0.40 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A 739 
   HIS   0.003   0.001   HIS A 867 
   PHE   0.019   0.001   PHE A 738 
   TYR   0.010   0.001   TYR A 845 
   ARG   0.007   0.000   ARG A 835 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 96
  average time/residue: 0.1888
  time to fit residues: 25.9841
Evaluate side-chains
  82 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.944 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0878
  time to fit residues: 2.0321
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0270
   chunk 69 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 109 optimal weight:   30.0000
   chunk 97 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8262  Z= 0.184
  Angle     :  0.482   6.467  11298  Z= 0.242
  Chirality :  0.039   0.144   1401
  Planarity :  0.003   0.033   1407
  Dihedral  :  5.854  63.513   1258
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.59 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1115
  helix:  1.48 (0.19), residues: 756
  sheet: -0.01 (0.71), residues: 69
  loop : -0.41 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 430 
   HIS   0.004   0.001   HIS A1024 
   PHE   0.015   0.001   PHE A 738 
   TYR   0.012   0.001   TYR A 378 
   ARG   0.003   0.000   ARG A 835 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1886
  time to fit residues: 26.5111
Evaluate side-chains
  84 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.830 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0788
  time to fit residues: 2.1828
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0270
   chunk 93 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8262  Z= 0.154
  Angle     :  0.494   9.049  11298  Z= 0.239
  Chirality :  0.038   0.175   1401
  Planarity :  0.003   0.032   1407
  Dihedral  :  5.685  64.544   1258
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.86 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1115
  helix:  1.65 (0.19), residues: 758
  sheet: -0.03 (0.70), residues: 69
  loop : -0.29 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 739 
   HIS   0.003   0.001   HIS A1024 
   PHE   0.014   0.001   PHE A 738 
   TYR   0.010   0.001   TYR A 378 
   ARG   0.010   0.000   ARG A 878 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1876
  time to fit residues: 25.5485
Evaluate side-chains
  86 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0747
  time to fit residues: 2.1695
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 109 optimal weight:   30.0000
   chunk 90 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0970
   chunk 57 optimal weight:   20.0000
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.4378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8262  Z= 0.135
  Angle     :  0.472   7.717  11298  Z= 0.231
  Chirality :  0.038   0.141   1401
  Planarity :  0.003   0.031   1407
  Dihedral  :  5.475  63.778   1258
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 18.81 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1115
  helix:  1.84 (0.19), residues: 752
  sheet: -0.08 (0.69), residues: 69
  loop : -0.27 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 739 
   HIS   0.002   0.000   HIS A1098 
   PHE   0.016   0.001   PHE A 738 
   TYR   0.009   0.001   TYR A 845 
   ARG   0.005   0.000   ARG A 265 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 94
  average time/residue: 0.1895
  time to fit residues: 25.8505
Evaluate side-chains
  86 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0800
  time to fit residues: 1.7533
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 108 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8262  Z= 0.180
  Angle     :  0.491   7.210  11298  Z= 0.240
  Chirality :  0.039   0.178   1401
  Planarity :  0.003   0.037   1407
  Dihedral  :  5.506  64.861   1258
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 19.62 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1115
  helix:  1.77 (0.19), residues: 757
  sheet: -0.07 (0.69), residues: 69
  loop : -0.18 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A 739 
   HIS   0.004   0.001   HIS A1024 
   PHE   0.013   0.001   PHE A 738 
   TYR   0.010   0.001   TYR A 378 
   ARG   0.009   0.000   ARG A 878 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 94
  average time/residue: 0.1971
  time to fit residues: 26.3569
Evaluate side-chains
  86 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.913 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0834
  time to fit residues: 1.6995
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8262  Z= 0.179
  Angle     :  0.490   9.651  11298  Z= 0.239
  Chirality :  0.039   0.191   1401
  Planarity :  0.003   0.035   1407
  Dihedral  :  5.438  65.026   1258
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 20.43 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1115
  helix:  1.86 (0.19), residues: 745
  sheet: -0.09 (0.68), residues: 69
  loop : -0.28 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A 739 
   HIS   0.003   0.001   HIS A1024 
   PHE   0.013   0.001   PHE A 738 
   TYR   0.010   0.001   TYR A 378 
   ARG   0.008   0.000   ARG A 878 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 90
  average time/residue: 0.1794
  time to fit residues: 23.6143
Evaluate side-chains
  87 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.920 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0913
  time to fit residues: 1.5495
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 104 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0570
   chunk 44 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0570
   chunk 91 optimal weight:    0.0050
   chunk 95 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.4032

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8262  Z= 0.135
  Angle     :  0.491  10.274  11298  Z= 0.237
  Chirality :  0.038   0.222   1401
  Planarity :  0.003   0.031   1407
  Dihedral  :  5.240  65.281   1258
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 20.84 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.26), residues: 1115
  helix:  2.00 (0.20), residues: 745
  sheet: -0.00 (0.68), residues: 69
  loop : -0.34 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 739 
   HIS   0.002   0.001   HIS A1098 
   PHE   0.014   0.001   PHE A 738 
   TYR   0.023   0.001   TYR A 230 
   ARG   0.005   0.000   ARG A 878 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1719
  time to fit residues: 23.5222
Evaluate side-chains
  86 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.045 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3411
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 112 optimal weight:   30.0000
   chunk 103 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8262  Z= 0.332
  Angle     :  0.592   9.986  11298  Z= 0.288
  Chirality :  0.042   0.182   1401
  Planarity :  0.003   0.032   1407
  Dihedral  :  5.617  65.105   1258
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 20.84 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1115
  helix:  1.54 (0.19), residues: 749
  sheet: -0.10 (0.68), residues: 69
  loop : -0.28 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A 739 
   HIS   0.005   0.001   HIS A1024 
   PHE   0.009   0.001   PHE A 738 
   TYR   0.024   0.001   TYR A 230 
   ARG   0.004   0.001   ARG A 265 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 81
  average time/residue: 0.1935
  time to fit residues: 22.5135
Evaluate side-chains
  78 residues out of total 978 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.904 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1013
  time to fit residues: 1.4002
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 89 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0970
   chunk 92 optimal weight:   20.0000
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.152103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.115905 restraints weight = 12202.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.41
r_work: 0.3489 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8262  Z= 0.147
  Angle     :  0.498  10.292  11298  Z= 0.241
  Chirality :  0.038   0.194   1401
  Planarity :  0.003   0.030   1407
  Dihedral  :  5.309  64.031   1258
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 21.11 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1115
  helix:  1.82 (0.20), residues: 747
  sheet:  0.05 (0.68), residues: 69
  loop : -0.33 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 739 
   HIS   0.003   0.001   HIS A1098 
   PHE   0.017   0.001   PHE A 236 
   TYR   0.018   0.001   TYR A 230 
   ARG   0.004   0.000   ARG A 265 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1719.42 seconds
wall clock time: 31 minutes 50.77 seconds (1910.77 seconds total)