Starting phenix.real_space_refine
on Fri Mar 15 18:11:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/03_2024/8p51_17436.pdb"
  }
  resolution = 3.55
  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=   0.003 sd=   0.038
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      35      5.16       5
     C    7779      2.51       5
     N    2197      2.21       5
     O    2378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR 1046": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 12389
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1574, 12389
          Classifications: {'peptide': 1574}
          Link IDs: {'PTRANS': 59, 'TRANS': 1514}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 16
    residue:
      pdb=" N   ILE A 931 " occ=0.37
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 931 " occ=0.00
    residue:
      pdb=" N   ALA A 949 " occ=0.94
      ... (3 atoms not shown)
      pdb=" CB  ALA A 949 " occ=0.21
    residue:
      pdb=" N   GLY A 972 " occ=0.51
      ... (2 atoms not shown)
      pdb=" O   GLY A 972 " occ=0.33
    residue:
      pdb=" N   ALA A 983 " occ=0.68
      ... (3 atoms not shown)
      pdb=" CB  ALA A 983 " occ=0.95
    residue:
      pdb=" N   SER A 987 " occ=0.90
      ... (4 atoms not shown)
      pdb=" OG  SER A 987 " occ=0.67
    residue:
      pdb=" N   ALA A 993 " occ=0.18
      ... (3 atoms not shown)
      pdb=" CB  ALA A 993 " occ=0.18
    residue:
      pdb=" N   ALA A1040 " occ=0.80
      ... (3 atoms not shown)
      pdb=" CB  ALA A1040 " occ=0.98
    residue:
      pdb=" N   GLN A1100 " occ=0.81
      ... (7 atoms not shown)
      pdb=" NE2 GLN A1100 " occ=0.23
    residue:
      pdb=" N   GLY A1103 " occ=0.91
      ... (2 atoms not shown)
      pdb=" O   GLY A1103 " occ=0.48
    residue:
      pdb=" N   ASP A1113 " occ=0.69
      ... (6 atoms not shown)
      pdb=" OD2 ASP A1113 " occ=0.64
    residue:
      pdb=" N   GLN A1120 " occ=0.79
      ... (7 atoms not shown)
      pdb=" NE2 GLN A1120 " occ=0.78
    residue:
      pdb=" N   SER A1160 " occ=0.14
      ... (4 atoms not shown)
      pdb=" OG  SER A1160 " occ=0.65
    ... (remaining 4 not shown)
  Time building chain proxies: 6.56, per 1000 atoms: 0.53
  Number of scatterers: 12389
  At special positions: 0
  Unit cell: (103.5, 116.1, 148.5, 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      35     16.00
     O    2378      8.00
     N    2197      7.00
     C    7779      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: 5.06
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2942

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 11 sheets defined
      56.3% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 35 through 55
    Processing helix  chain 'A' and resid 55 through 64
      removed outlier: 3.536A  pdb=" N   GLN A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 86
    Processing helix  chain 'A' and resid 93 through 132
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 147 through 170
      removed outlier: 4.413A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 202
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 4.640A  pdb=" N   ALA A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ALA A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 4.122A  pdb=" N   ARG A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.529A  pdb=" N   TYR A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 4.093A  pdb=" N   VAL A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 390
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 418 through 425
    Processing helix  chain 'A' and resid 465 through 489
      removed outlier: 3.816A  pdb=" N   SER A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 517
      removed outlier: 3.808A  pdb=" N   ARG A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.523A  pdb=" N   ARG A 567 " --> pdb=" O   PRO A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 577
      removed outlier: 6.218A  pdb=" N   ALA A 577 " --> pdb=" O   LYS A 574 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 574 through 577'
    Processing helix  chain 'A' and resid 578 through 583
      removed outlier: 4.157A  pdb=" N   LEU A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A 583 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 583'
    Processing helix  chain 'A' and resid 586 through 589
    Processing helix  chain 'A' and resid 590 through 598
    Processing helix  chain 'A' and resid 598 through 623
      removed outlier: 4.244A  pdb=" N   GLU A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ALA A 612 " --> pdb=" O   ARG A 608 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   GLU A 613 " --> pdb=" O   ALA A 609 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR A 614 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 654 through 658
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 665 through 674
      removed outlier: 3.544A  pdb=" N   LEU A 674 " --> pdb=" O   GLU A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 698
      removed outlier: 3.948A  pdb=" N   LEU A 686 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS A 688 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
      Proline residue:  A 692  - end of helix
      removed outlier: 3.571A  pdb=" N   PHE A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   SER A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 731
    Processing helix  chain 'A' and resid 735 through 740
      removed outlier: 3.573A  pdb=" N   ARG A 740 " --> pdb=" O   GLN A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 756
    Processing helix  chain 'A' and resid 763 through 773
    Processing helix  chain 'A' and resid 781 through 789
    Processing helix  chain 'A' and resid 790 through 795
    Processing helix  chain 'A' and resid 800 through 818
    Processing helix  chain 'A' and resid 823 through 834
      removed outlier: 4.915A  pdb=" N   VAL A 829 " --> pdb=" O   GLU A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 857
      removed outlier: 3.673A  pdb=" N   GLU A 855 " --> pdb=" O   LYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 878
      removed outlier: 3.922A  pdb=" N   ARG A 872 " --> pdb=" O   GLY A 868 " (cutoff:3.500A)
      Proline residue:  A 875  - end of helix
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 902 through 906
    Processing helix  chain 'A' and resid 930 through 937
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 949 through 953
    Processing helix  chain 'A' and resid 985 through 988
    Processing helix  chain 'A' and resid 1052 through 1056
    Processing helix  chain 'A' and resid 1065 through 1070
      removed outlier: 3.908A  pdb=" N   TYR A1069 " --> pdb=" O   ASP A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1152
      removed outlier: 3.953A  pdb=" N   GLN A1133 " --> pdb=" O   ARG A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1173 through 1175
      No H-bonds generated for 'chain 'A' and resid 1173 through 1175'
    Processing helix  chain 'A' and resid 1176 through 1209
      removed outlier: 3.624A  pdb=" N   ILE A1190 " --> pdb=" O   VAL A1186 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASP A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLN A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A1197 " --> pdb=" O   ASP A1193 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A1200 " --> pdb=" O   GLN A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1259
      removed outlier: 4.129A  pdb=" N   ILE A1217 " --> pdb=" O   ARG A1213 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLN A1219 " --> pdb=" O   ASP A1215 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   GLN A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A1221 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR A1231 " --> pdb=" O   THR A1227 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   THR A1237 " --> pdb=" O   ALA A1233 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   VAL A1238 " --> pdb=" O   GLN A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1263
    Processing helix  chain 'A' and resid 1281 through 1289
    Processing helix  chain 'A' and resid 1298 through 1308
      removed outlier: 4.304A  pdb=" N   SER A1302 " --> pdb=" O   GLY A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1331
    Processing helix  chain 'A' and resid 1335 through 1358
    Processing helix  chain 'A' and resid 1361 through 1373
      removed outlier: 3.852A  pdb=" N   PHE A1365 " --> pdb=" O   GLN A1361 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER A1366 " --> pdb=" O   THR A1362 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLU A1367 " --> pdb=" O   ALA A1363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1396
      removed outlier: 3.950A  pdb=" N   GLY A1395 " --> pdb=" O   ASP A1391 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ARG A1396 " --> pdb=" O   ARG A1392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1391 through 1396'
    Processing helix  chain 'A' and resid 1396 through 1429
      removed outlier: 3.759A  pdb=" N   ARG A1402 " --> pdb=" O   TYR A1398 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL A1406 " --> pdb=" O   ARG A1402 " (cutoff:3.500A)
      removed outlier: 8.600A  pdb=" N   GLU A1413 " --> pdb=" O   ALA A1409 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   ALA A1414 " --> pdb=" O   SER A1410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1443
    Processing helix  chain 'A' and resid 1448 through 1453
    Processing helix  chain 'A' and resid 1463 through 1473
    Processing helix  chain 'A' and resid 1515 through 1528
      removed outlier: 3.529A  pdb=" N   GLN A1525 " --> pdb=" O   ARG A1521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1531 through 1536
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 3.765A  pdb=" N   ALA A1558 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1576 through 1589
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236
      removed outlier: 7.640A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 241 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 236 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 363 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339
      removed outlier: 5.357A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 363 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 307 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261
    Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454
    Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722
    Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948
      removed outlier: 6.729A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948
      removed outlier: 6.729A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014
      removed outlier: 6.609A  pdb=" N   SER A1037 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL A1060 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1376 through 1379
      removed outlier: 4.286A  pdb=" N   PHE A1376 " --> pdb=" O   ALA A1512 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1462
      removed outlier: 5.020A  pdb=" N   GLY A1459 " --> pdb=" O   LEU A1549 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A1549 " --> pdb=" O   GLY A1459 " (cutoff:3.500A)

    703 hydrogen bonds defined for protein.
    2019 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.16

  Time building geometry restraints manager: 5.49 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: 4230
        1.34 -     1.46: 2258
        1.46 -     1.57: 6061
        1.57 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 12618
  Sorted by residual:
  bond pdb=" CD  ARG A1530 "
       pdb=" NE  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.53e+00
  bond pdb=" CD  ARG A1209 "
       pdb=" NE  ARG A1209 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.45e+00
  bond pdb=" CA  ARG A1530 "
       pdb=" CB  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.529  1.507  0.022 1.40e-02 5.10e+03 2.38e+00
  bond pdb=" C   TYR A1398 "
       pdb=" N   PRO A1399 "
    ideal  model  delta    sigma   weight residual
    1.336  1.319  0.017 1.20e-02 6.94e+03 2.05e+00
  bond pdb=" CB  TRP A 805 "
       pdb=" CG  TRP A 805 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.01e+00
  ... (remaining 12613 not shown)

  Histogram of bond angle deviations from ideal:
       99.06 -   106.07: 268
      106.07 -   113.07: 6720
      113.07 -   120.07: 4638
      120.07 -   127.08: 5353
      127.08 -   134.08: 101
  Bond angle restraints: 17080
  Sorted by residual:
  angle pdb=" N   VAL A 969 "
        pdb=" CA  VAL A 969 "
        pdb=" C   VAL A 969 "
      ideal   model   delta    sigma   weight residual
     113.71  109.85    3.86 9.50e-01 1.11e+00 1.65e+01
  angle pdb=" C   GLU A1206 "
        pdb=" N   ASN A1207 "
        pdb=" CA  ASN A1207 "
      ideal   model   delta    sigma   weight residual
     121.52  115.83    5.69 1.84e+00 2.95e-01 9.56e+00
  angle pdb=" CA  ARG A1214 "
        pdb=" CB  ARG A1214 "
        pdb=" CG  ARG A1214 "
      ideal   model   delta    sigma   weight residual
     114.10  120.09   -5.99 2.00e+00 2.50e-01 8.97e+00
  angle pdb=" N   SER A 301 "
        pdb=" CA  SER A 301 "
        pdb=" C   SER A 301 "
      ideal   model   delta    sigma   weight residual
     109.81  115.95   -6.14 2.21e+00 2.05e-01 7.71e+00
  angle pdb=" CA  GLN A  65 "
        pdb=" CB  GLN A  65 "
        pdb=" CG  GLN A  65 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.59e+00
  ... (remaining 17075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7066
       17.95 -    35.89: 471
       35.89 -    53.84: 63
       53.84 -    71.79: 36
       71.79 -    89.74: 15
  Dihedral angle restraints: 7651
    sinusoidal: 3078
      harmonic: 4573
  Sorted by residual:
  dihedral pdb=" CA  PRO A1014 "
           pdb=" C   PRO A1014 "
           pdb=" N   LYS A1015 "
           pdb=" CA  LYS A1015 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ASN A 984 "
           pdb=" C   ASN A 984 "
           pdb=" N   ASP A 985 "
           pdb=" CA  ASP A 985 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  SER A 394 "
           pdb=" C   SER A 394 "
           pdb=" N   PHE A 395 "
           pdb=" CA  PHE A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.77   28.23     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 7648 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1373
       0.050 -    0.100: 423
       0.100 -    0.149: 91
       0.149 -    0.199: 5
       0.199 -    0.249: 1
  Chirality restraints: 1893
  Sorted by residual:
  chirality pdb=" CA  ARG A1209 "
            pdb=" N   ARG A1209 "
            pdb=" C   ARG A1209 "
            pdb=" CB  ARG A1209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LYS A1357 "
            pdb=" N   LYS A1357 "
            pdb=" C   LYS A1357 "
            pdb=" CB  LYS A1357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.59e-01
  chirality pdb=" CA  PHE A 827 "
            pdb=" N   PHE A 827 "
            pdb=" C   PHE A 827 "
            pdb=" CB  PHE A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.39e-01
  ... (remaining 1890 not shown)

  Planarity restraints: 2259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1578 "   -0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   SER A1578 "    0.067 2.00e-02 2.50e+03
        pdb=" O   SER A1578 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER A1579 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1408 "   -0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   LEU A1408 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LEU A1408 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A1409 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1405 "    0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   THR A1405 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   THR A1405 "    0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A1406 "    0.020 2.00e-02 2.50e+03
  ... (remaining 2256 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 215
        2.67 -     3.23: 12886
        3.23 -     3.79: 18643
        3.79 -     4.34: 25100
        4.34 -     4.90: 40789
  Nonbonded interactions: 97633
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 144 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.113 2.440
  nonbonded pdb=" OG  SER A1054 "
            pdb=" OD2 ASP A1065 "
     model   vdw
     2.165 2.440
  nonbonded pdb=" OH  TYR A1137 "
            pdb=" OE2 GLU A1241 "
     model   vdw
     2.178 2.440
  nonbonded pdb=" OG  SER A 500 "
            pdb=" OE1 GLU A 502 "
     model   vdw
     2.194 2.440
  nonbonded pdb=" OD1 ASN A  13 "
            pdb=" NH1 ARG A  37 "
     model   vdw
     2.257 2.520
  ... (remaining 97628 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=0.00 max=1.00 mean=0.97
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  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:          6.310
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     36.470
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
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   0.044  12618  Z= 0.414
  Angle     :  0.827   6.865  17080  Z= 0.472
  Chirality :  0.048   0.249   1893
  Planarity :  0.009   0.101   2259
  Dihedral  : 13.504  89.737   4709
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -1.93 (0.19), residues: 1570
  helix: -1.25 (0.16), residues: 786
  sheet: -0.49 (0.38), residues: 160
  loop : -1.33 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A1251 
 HIS   0.008   0.002   HIS A1370 
 PHE   0.022   0.002   PHE A  30 
 TYR   0.026   0.005   TYR A 820 
 ARG   0.022   0.003   ARG A 817 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.3278
  time to fit residues: 56.5964
Evaluate side-chains
  62 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 40 optimal weight:   20.0000
   chunk 80 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 142 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A  52 GLN
A 288 GLN
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 GLN
A 862 GLN
A1052 ASN
A1207 ASN
A1446 HIS
A1486 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12618  Z= 0.204
  Angle     :  0.661   9.276  17080  Z= 0.347
  Chirality :  0.041   0.156   1893
  Planarity :  0.005   0.038   2259
  Dihedral  :  5.592  20.764   1737
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  4.67 %
    Favored  : 94.58 %
  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:  0.19 (0.21), residues: 1570
  helix:  0.73 (0.19), residues: 808
  sheet: -0.26 (0.38), residues: 162
  loop : -0.46 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 124 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.019   0.001   PHE A 395 
 TYR   0.018   0.002   TYR A1046 
 ARG   0.016   0.001   ARG A1392 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1176 ILE cc_start: 0.9764 (pt) cc_final: 0.9373 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 84
  average time/residue: 0.3121
  time to fit residues: 38.9963
Evaluate side-chains
  63 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 39 optimal weight:   30.0000
   chunk 142 optimal weight:    3.9990
   chunk 154 optimal weight:    2.9990
   chunk 127 optimal weight:    8.9990
   chunk 141 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 114 optimal weight:    8.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12618  Z= 0.198
  Angle     :  0.595  10.240  17080  Z= 0.308
  Chirality :  0.039   0.170   1893
  Planarity :  0.004   0.044   2259
  Dihedral  :  5.057  21.231   1737
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.25 %
    Favored  : 93.07 %
  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:  0.66 (0.22), residues: 1570
  helix:  1.20 (0.19), residues: 808
  sheet: -0.19 (0.40), residues: 157
  loop : -0.32 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 605 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.015   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A1046 
 ARG   0.005   0.000   ARG A 487 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1176 ILE cc_start: 0.9744 (pt) cc_final: 0.9318 (mm)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.2499
  time to fit residues: 27.6604
Evaluate side-chains
  66 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 141 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 143 optimal weight:   10.0000
   chunk 151 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12618  Z= 0.255
  Angle     :  0.602   9.122  17080  Z= 0.311
  Chirality :  0.040   0.168   1893
  Planarity :  0.004   0.042   2259
  Dihedral  :  4.827  21.584   1737
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.57 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.91 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.22), residues: 1570
  helix:  1.42 (0.19), residues: 795
  sheet: -0.20 (0.40), residues: 159
  loop : -0.32 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 124 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.015   0.001   PHE A 497 
 TYR   0.016   0.001   TYR A 473 
 ARG   0.008   0.000   ARG A 125 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: A 1176 ILE cc_start: 0.9745 (pt) cc_final: 0.9340 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 67
  average time/residue: 0.2521
  time to fit residues: 26.5911
Evaluate side-chains
  64 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1215 ASP
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 129 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 136 optimal weight:    0.6980
   chunk 38 optimal weight:   20.0000
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 509 GLN
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12618  Z= 0.183
  Angle     :  0.571  11.879  17080  Z= 0.291
  Chirality :  0.038   0.172   1893
  Planarity :  0.004   0.041   2259
  Dihedral  :  4.607  20.855   1737
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.50 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.28 %
    Favored  : 90.51 %
  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:  0.96 (0.22), residues: 1570
  helix:  1.55 (0.19), residues: 795
  sheet: -0.10 (0.40), residues: 159
  loop : -0.28 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 124 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.015   0.001   TYR A 768 
 ARG   0.003   0.000   ARG A 308 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  652 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8187 (mp)
REVERT: A 1176 ILE cc_start: 0.9741 (pt) cc_final: 0.9333 (mm)
  outliers start: 16
  outliers final: 12
  residues processed: 72
  average time/residue: 0.2211
  time to fit residues: 25.6200
Evaluate side-chains
  67 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1203 LYS
Chi-restraints excluded: chain A residue 1215 ASP
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 136 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0270
   chunk 89 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 151 optimal weight:    0.9990
   chunk 126 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 146 optimal weight:    0.9990
   overall best weight:    0.5642

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12618  Z= 0.127
  Angle     :  0.555  11.371  17080  Z= 0.278
  Chirality :  0.038   0.172   1893
  Planarity :  0.003   0.042   2259
  Dihedral  :  4.328  20.689   1737
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.31 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.34 %
    Favored  : 89.83 %
  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:  1.22 (0.22), residues: 1570
  helix:  1.75 (0.19), residues: 795
  sheet: -0.01 (0.40), residues: 162
  loop : -0.14 (0.27), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 124 
 HIS   0.009   0.001   HIS A  63 
 PHE   0.018   0.001   PHE A 277 
 TYR   0.014   0.001   TYR A 768 
 ARG   0.004   0.000   ARG A1392 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 1.498 
Fit side-chains
   revert: symmetry clash
REVERT: A 1176 ILE cc_start: 0.9724 (pt) cc_final: 0.9372 (mm)
  outliers start: 11
  outliers final: 5
  residues processed: 74
  average time/residue: 0.2427
  time to fit residues: 27.6960
Evaluate side-chains
  65 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 127 optimal weight:    9.9990
   chunk 84 optimal weight:    0.9990
   chunk 151 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 92 optimal weight:    0.4980
   chunk 69 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 GLN
A1130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12618  Z= 0.193
  Angle     :  0.571  11.589  17080  Z= 0.285
  Chirality :  0.038   0.162   1893
  Planarity :  0.003   0.041   2259
  Dihedral  :  4.251  20.306   1737
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.99 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.09 %
    Favored  : 88.86 %
  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:  1.28 (0.22), residues: 1570
  helix:  1.83 (0.19), residues: 795
  sheet: -0.11 (0.39), residues: 163
  loop : -0.10 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1090 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.018   0.001   PHE A 395 
 TYR   0.014   0.001   TYR A1046 
 ARG   0.004   0.000   ARG A1392 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1176 ILE cc_start: 0.9724 (pt) cc_final: 0.9367 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 74
  average time/residue: 0.2219
  time to fit residues: 26.3384
Evaluate side-chains
  71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  323 ASN
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 96 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 14 optimal weight:    0.2980
   chunk 118 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12618  Z= 0.168
  Angle     :  0.566  11.717  17080  Z= 0.280
  Chirality :  0.038   0.156   1893
  Planarity :  0.003   0.040   2259
  Dihedral  :  4.209  19.947   1737
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.25 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.64 %
    Favored  : 88.86 %
  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:  1.29 (0.22), residues: 1570
  helix:  1.83 (0.19), residues: 797
  sheet: -0.17 (0.39), residues: 163
  loop : -0.08 (0.27), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 124 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.009   0.001   PHE A 480 
 TYR   0.013   0.001   TYR A1046 
 ARG   0.004   0.000   ARG A1213 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.3865 (m-80)
REVERT: A  652 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8241 (mp)
  outliers start: 20
  outliers final: 11
  residues processed: 75
  average time/residue: 0.2401
  time to fit residues: 28.3539
Evaluate side-chains
  71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1172 ASP
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    3.9990
   chunk 141 optimal weight:    2.9990
   chunk 144 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 127 optimal weight:    0.0270
   chunk 133 optimal weight:    0.7980
   chunk 140 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   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 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12618  Z= 0.144
  Angle     :  0.566  11.358  17080  Z= 0.278
  Chirality :  0.038   0.136   1893
  Planarity :  0.003   0.040   2259
  Dihedral  :  4.113  22.763   1737
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.25 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.02 %
    Favored  : 88.86 %
  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:  1.30 (0.22), residues: 1570
  helix:  1.80 (0.19), residues: 803
  sheet: -0.26 (0.38), residues: 170
  loop : -0.00 (0.27), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 124 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.033   0.001   PHE A 277 
 TYR   0.013   0.001   TYR A1046 
 ARG   0.003   0.000   ARG A1392 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8247 (mp)
  outliers start: 15
  outliers final: 10
  residues processed: 73
  average time/residue: 0.2582
  time to fit residues: 28.7451
Evaluate side-chains
  69 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1172 ASP
Chi-restraints excluded: chain A residue 1392 ARG
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 149 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 156 optimal weight:    0.7980
   chunk 143 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12618  Z= 0.252
  Angle     :  0.628  11.811  17080  Z= 0.310
  Chirality :  0.039   0.146   1893
  Planarity :  0.003   0.039   2259
  Dihedral  :  4.244  24.602   1737
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.44 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.77 %
    Favored  : 88.48 %
  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:  1.22 (0.22), residues: 1570
  helix:  1.77 (0.19), residues: 801
  sheet: -0.34 (0.39), residues: 169
  loop : -0.07 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1251 
 HIS   0.006   0.001   HIS A  63 
 PHE   0.021   0.001   PHE A 277 
 TYR   0.013   0.001   TYR A1504 
 ARG   0.008   0.000   ARG A 105 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8277 (mp)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.2243
  time to fit residues: 23.0620
Evaluate side-chains
  65 residues out of total 1328 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  196 TYR
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1172 ASP
Chi-restraints excluded: chain A residue 1572 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 114 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   chunk 124 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 128 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 GLN
A1047 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.077420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.050845 restraints weight = 55806.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.052574 restraints weight = 29643.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.053697 restraints weight = 20830.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      109 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12618  Z= 0.405
  Angle     :  0.732  12.296  17080  Z= 0.366
  Chirality :  0.042   0.158   1893
  Planarity :  0.004   0.039   2259
  Dihedral  :  4.620  24.295   1737
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.01 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.69 %
    Favored  : 88.25 %
  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:  0.82 (0.22), residues: 1570
  helix:  1.46 (0.19), residues: 796
  sheet: -0.68 (0.38), residues: 169
  loop : -0.21 (0.27), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1251 
 HIS   0.006   0.001   HIS A1370 
 PHE   0.024   0.002   PHE A 277 
 TYR   0.016   0.002   TYR A1504 
 ARG   0.004   0.001   ARG A 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2207.49 seconds
wall clock time: 40 minutes 47.03 seconds (2447.03 seconds total)