Starting phenix.real_space_refine
on Fri Feb 14 13:08:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uy0_20945/02_2025/6uy0_20945.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    6266      2.51       5
     N    1607      2.21       5
     O    1757      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9684
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1210, 9540
          Classifications: {'peptide': 1210}
          Link IDs: {'PTRANS': 44, 'TRANS': 1165}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 144
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 6.01, per 1000 atoms: 0.62
  Number of scatterers: 9684
  At special positions: 0
  Unit cell: (143.17, 98.88, 83.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      47     16.00
     P       5     15.00
     Mg      2     11.99
     O    1757      8.00
     N    1607      7.00
     C    6266      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  - 3.00
        Amino acid           : True  - 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: 2.29
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2282

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      68.1% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.714A  pdb=" N   THR A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 234
    Processing helix  chain 'A' and resid 245 through 248
    Processing helix  chain 'A' and resid 249 through 268
      Proline residue:  A 255  - end of helix
      removed outlier: 3.539A  pdb=" N   LYS A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 326 through 355
      removed outlier: 3.763A  pdb=" N   LEU A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
      removed outlier: 3.660A  pdb=" N   ASN A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 408
      removed outlier: 3.948A  pdb=" N   GLY A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   TYR A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A 365 " --> pdb=" O   TRP A 361 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR A 366 " --> pdb=" O   GLN A 362 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 367 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 408 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
      removed outlier: 3.591A  pdb=" N   SER A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 441
      removed outlier: 3.819A  pdb=" N   ASP A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ALA A 431 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN A 432 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   THR A 439 " --> pdb=" O   MET A 435 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   TYR A 440 " --> pdb=" O   ASP A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 462
      removed outlier: 3.763A  pdb=" N   SER A 446 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
      Proline residue:  A 448  - end of helix
      removed outlier: 3.593A  pdb=" N   LEU A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 511
      removed outlier: 3.573A  pdb=" N   VAL A 477 " --> pdb=" O   MET A 473 " (cutoff:3.500A)
      Proline residue:  A 478  - end of helix
      removed outlier: 3.783A  pdb=" N   THR A 489 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 490 " --> pdb=" O   LYS A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 519
    Processing helix  chain 'A' and resid 520 through 555
      removed outlier: 3.696A  pdb=" N   CYS A 555 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 572
      removed outlier: 3.552A  pdb=" N   LEU A 559 " --> pdb=" O   CYS A 555 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 567 " --> pdb=" O   SER A 563 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A 568 " --> pdb=" O   THR A 564 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 590
      removed outlier: 3.867A  pdb=" N   VAL A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 597
      removed outlier: 4.006A  pdb=" N   LEU A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 621
      removed outlier: 3.609A  pdb=" N   VAL A 602 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 630
      removed outlier: 3.594A  pdb=" N   SER A 629 " --> pdb=" O   ASP A 626 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 630 " --> pdb=" O   PRO A 627 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 626 through 630'
    Processing helix  chain 'A' and resid 683 through 692
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 733 through 744
    Processing helix  chain 'A' and resid 746 through 753
    Processing helix  chain 'A' and resid 769 through 785
      removed outlier: 3.636A  pdb=" N   ALA A 781 " --> pdb=" O   SER A 777 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP A 785 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 810
    Processing helix  chain 'A' and resid 831 through 835
    Processing helix  chain 'A' and resid 851 through 858
    Processing helix  chain 'A' and resid 860 through 870
      removed outlier: 3.578A  pdb=" N   GLU A 864 " --> pdb=" O   GLY A 860 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 868 " --> pdb=" O   GLU A 864 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A 869 " --> pdb=" O   PHE A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 970
      removed outlier: 4.017A  pdb=" N   TYR A 962 " --> pdb=" O   LYS A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1000
      removed outlier: 3.539A  pdb=" N   SER A 974 " --> pdb=" O   GLY A 970 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASP A1000 " --> pdb=" O   SER A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1058
      removed outlier: 3.988A  pdb=" N   SER A1016 " --> pdb=" O   GLN A1012 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL A1017 " --> pdb=" O   VAL A1013 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER A1037 " --> pdb=" O   SER A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1059 through 1066
      removed outlier: 3.927A  pdb=" N   PHE A1063 " --> pdb=" O   PRO A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1111
      removed outlier: 3.805A  pdb=" N   LEU A1071 " --> pdb=" O   PRO A1067 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ARG A1074 " --> pdb=" O   ASN A1070 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLU A1078 " --> pdb=" O   ARG A1074 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   LEU A1079 " --> pdb=" O   PHE A1075 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE A1086 " --> pdb=" O   VAL A1082 " (cutoff:3.500A)
      Proline residue:  A1087  - end of helix
      removed outlier: 3.568A  pdb=" N   ILE A1106 " --> pdb=" O   GLY A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1115
      removed outlier: 3.787A  pdb=" N   ALA A1115 " --> pdb=" O   PRO A1112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1112 through 1115'
    Processing helix  chain 'A' and resid 1117 through 1147
      removed outlier: 3.536A  pdb=" N   TYR A1125 " --> pdb=" O   LEU A1121 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A1134 " --> pdb=" O   ARG A1130 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A1135 " --> pdb=" O   PHE A1131 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A1138 " --> pdb=" O   ALA A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1147 through 1160
      removed outlier: 3.748A  pdb=" N   TYR A1151 " --> pdb=" O   ARG A1147 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A1159 " --> pdb=" O   ASN A1155 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY A1160 " --> pdb=" O   GLU A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1160 through 1168
    Processing helix  chain 'A' and resid 1169 through 1220
      removed outlier: 3.778A  pdb=" N   GLU A1183 " --> pdb=" O   LEU A1179 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ASN A1184 " --> pdb=" O   LYS A1180 " (cutoff:3.500A)
      Proline residue:  A1190  - end of helix
    Processing helix  chain 'A' and resid 1225 through 1257
      removed outlier: 3.688A  pdb=" N   GLY A1230 " --> pdb=" O   ALA A1226 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   LEU A1231 " --> pdb=" O   GLY A1227 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A1232 " --> pdb=" O   LEU A1228 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   VAL A1233 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   SER A1234 " --> pdb=" O   GLY A1230 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TYR A1235 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLN A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A1240 " --> pdb=" O   SER A1236 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ARG A1248 " --> pdb=" O   ASN A1244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1265
      removed outlier: 3.556A  pdb=" N   GLU A1265 " --> pdb=" O   GLU A1261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1332 through 1340
      removed outlier: 3.587A  pdb=" N   THR A1336 " --> pdb=" O   LYS A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1361 through 1367
    Processing helix  chain 'A' and resid 1383 through 1388
      removed outlier: 3.548A  pdb=" N   LEU A1387 " --> pdb=" O   LEU A1383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1394 through 1405
      removed outlier: 3.584A  pdb=" N   VAL A1398 " --> pdb=" O   SER A1394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1407 through 1413
    Processing helix  chain 'A' and resid 1430 through 1446
      removed outlier: 3.596A  pdb=" N   LEU A1436 " --> pdb=" O   GLY A1432 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ARG A1445 " --> pdb=" O   ARG A1441 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A1446 " --> pdb=" O   ALA A1442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1460 through 1475
    Processing helix  chain 'A' and resid 1486 through 1490
    Processing helix  chain 'A' and resid 1509 through 1517
      removed outlier: 3.644A  pdb=" N   ARG A1517 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1519 through 1528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 669
      removed outlier: 7.244A  pdb=" N   HIS A 662 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR A 650 " --> pdb=" O   HIS A 662 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ILE A 664 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ILE A 644 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL A 704 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   VAL A 646 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL A 702 " --> pdb=" O   VAL A 646 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ASN A 648 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLY A 700 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   THR A 650 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.565A  pdb=" N   ALA A 709 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   ASP A 792 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   VAL A 711 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   TYR A 789 " --> pdb=" O   LEU A 823 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   VAL A 825 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   LEU A 791 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL A 674 " --> pdb=" O   LEU A 824 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA A 675 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   MET A 841 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A 677 " --> pdb=" O   MET A 841 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 848 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   SER A 842 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      removed outlier: 5.815A  pdb=" N   ILE A 846 " --> pdb=" O   SER A 842 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1309 through 1316
      removed outlier: 6.432A  pdb=" N   LYS A1310 " --> pdb=" O   GLY A1298 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   GLY A1298 " --> pdb=" O   LYS A1310 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ILE A1312 " --> pdb=" O   ASP A1296 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A1314 " --> pdb=" O   PHE A1294 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   TYR A1297 " --> pdb=" O   GLU A1347 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLU A1347 " --> pdb=" O   TYR A1297 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1369 through 1372
      removed outlier: 3.584A  pdb=" N   ARG A1495 " --> pdb=" O   LYS A1321 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1381 through 1382

    572 hydrogen bonds defined for protein.
    1692 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.61

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1820
        1.34 -     1.46: 2296
        1.46 -     1.58: 5689
        1.58 -     1.70: 8
        1.70 -     1.82: 79
  Bond restraints: 9892
  Sorted by residual:
  bond pdb=" C4  ATP A1601 "
       pdb=" C5  ATP A1601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.91e+01
  bond pdb=" C5  ATP A1601 "
       pdb=" C6  ATP A1601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.477 -0.068 1.00e-02 1.00e+04 4.61e+01
  bond pdb=" C8  ATP A1601 "
       pdb=" N7  ATP A1601 "
    ideal  model  delta    sigma   weight residual
    1.310  1.356 -0.046 1.00e-02 1.00e+04 2.12e+01
  bond pdb=" N   VAL A 668 "
       pdb=" CA  VAL A 668 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 8.70e-03 1.32e+04 2.11e+01
  bond pdb=" N   VAL A 711 "
       pdb=" CA  VAL A 711 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 8.60e-03 1.35e+04 1.96e+01
  ... (remaining 9887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9056
        1.78 -     3.56: 3570
        3.56 -     5.34: 776
        5.34 -     7.12: 41
        7.12 -     8.90: 7
  Bond angle restraints: 13450
  Sorted by residual:
  angle pdb=" C5  ATP A1601 "
        pdb=" C4  ATP A1601 "
        pdb=" N3  ATP A1601 "
      ideal   model   delta    sigma   weight residual
     126.80  118.75    8.05 1.00e+00 1.00e+00 6.48e+01
  angle pdb=" PB  ATP A1601 "
        pdb=" O3B ATP A1601 "
        pdb=" PG  ATP A1601 "
      ideal   model   delta    sigma   weight residual
     139.87  131.94    7.93 1.00e+00 1.00e+00 6.30e+01
  angle pdb=" PA  ATP A1601 "
        pdb=" O3A ATP A1601 "
        pdb=" PB  ATP A1601 "
      ideal   model   delta    sigma   weight residual
     136.83  129.85    6.98 1.00e+00 1.00e+00 4.87e+01
  angle pdb=" N3  ATP A1601 "
        pdb=" C4  ATP A1601 "
        pdb=" N9  ATP A1601 "
      ideal   model   delta    sigma   weight residual
     127.04  134.79   -7.75 1.15e+00 7.59e-01 4.56e+01
  angle pdb=" CA  GLY A 762 "
        pdb=" C   GLY A 762 "
        pdb=" O   GLY A 762 "
      ideal   model   delta    sigma   weight residual
     122.23  117.85    4.38 6.90e-01 2.10e+00 4.03e+01
  ... (remaining 13445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.50: 5670
       21.50 -    43.01: 357
       43.01 -    64.51: 43
       64.51 -    86.02: 5
       86.02 -   107.52: 2
  Dihedral angle restraints: 6077
    sinusoidal: 2550
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" O1B ADP A1602 "
           pdb=" O3A ADP A1602 "
           pdb=" PB  ADP A1602 "
           pdb=" PA  ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -167.52  107.52     1      2.00e+01 2.50e-03 3.12e+01
  dihedral pdb=" C5' ADP A1602 "
           pdb=" O5' ADP A1602 "
           pdb=" PA  ADP A1602 "
           pdb=" O2A ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -163.32  103.32     1      2.00e+01 2.50e-03 2.95e+01
  dihedral pdb=" CA  ASN A 575 "
           pdb=" C   ASN A 575 "
           pdb=" N   ILE A 576 "
           pdb=" CA  ILE A 576 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.68  -22.32     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 6074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 559
       0.045 -    0.090: 515
       0.090 -    0.134: 365
       0.134 -    0.179: 114
       0.179 -    0.224: 21
  Chirality restraints: 1574
  Sorted by residual:
  chirality pdb=" CA  ILE A1483 "
            pdb=" N   ILE A1483 "
            pdb=" C   ILE A1483 "
            pdb=" CB  ILE A1483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  PRO A1119 "
            pdb=" N   PRO A1119 "
            pdb=" C   PRO A1119 "
            pdb=" CB  PRO A1119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  VAL A1451 "
            pdb=" N   VAL A1451 "
            pdb=" C   VAL A1451 "
            pdb=" CB  VAL A1451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1571 not shown)

  Planarity restraints: 1654
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 869 "   -0.021 2.00e-02 2.50e+03   1.11e-02 2.47e+00
        pdb=" CG  TYR A 869 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 869 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 869 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 869 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 869 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 869 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 869 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1481 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   LEU A1481 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   LEU A1481 "    0.008 2.00e-02 2.50e+03
        pdb=" N   THR A1482 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1277 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" C   ILE A1277 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ILE A1277 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLN A1278 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1651 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 9
        2.47 -     3.08: 5508
        3.08 -     3.68: 14748
        3.68 -     4.29: 19551
        4.29 -     4.90: 35672
  Nonbonded interactions: 75488
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1333 "
            pdb="MG    MG A1604 "
     model   vdw
     1.861 2.170
  nonbonded pdb=" OG  SER A 685 "
            pdb="MG    MG A1603 "
     model   vdw
     1.863 2.170
  nonbonded pdb=" O1G ATP A1601 "
            pdb="MG    MG A1603 "
     model   vdw
     1.912 2.170
  nonbonded pdb=" O2B ADP A1602 "
            pdb="MG    MG A1604 "
     model   vdw
     1.982 2.170
  nonbonded pdb=" O1B ATP A1601 "
            pdb="MG    MG A1603 "
     model   vdw
     2.028 2.170
  ... (remaining 75483 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:             5.400
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.290
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
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      :  0.014   0.077   9892  Z= 0.899
  Angle     :  1.845   8.902  13450  Z= 1.415
  Chirality :  0.083   0.224   1574
  Planarity :  0.003   0.013   1654
  Dihedral  : 13.733 107.522   3795
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.19), residues: 1202
  helix: -1.20 (0.16), residues: 716
  sheet: -1.37 (0.52), residues: 76
  loop : -2.44 (0.25), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 963 
 HIS   0.007   0.001   HIS A 382 
 PHE   0.018   0.002   PHE A1379 
 TYR   0.021   0.002   TYR A 869 
 ARG   0.005   0.001   ARG A 775 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.7213 (tt0) cc_final: 0.6612 (tp40)
REVERT: A  234 GLN cc_start: 0.6526 (mp10) cc_final: 0.6196 (pp30)
REVERT: A  361 TRP cc_start: 0.7268 (p-90) cc_final: 0.6908 (p-90)
REVERT: A  648 ASN cc_start: 0.7215 (t0) cc_final: 0.6837 (m-40)
REVERT: A  670 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7509 (tp30)
REVERT: A  679 GLN cc_start: 0.7154 (mm110) cc_final: 0.6709 (mm-40)
REVERT: A  733 GLN cc_start: 0.5598 (mp10) cc_final: 0.5224 (mt0)
REVERT: A  796 SER cc_start: 0.8245 (t) cc_final: 0.7885 (p)
REVERT: A  835 MET cc_start: 0.7563 (mmt) cc_final: 0.7199 (mmt)
REVERT: A  851 SER cc_start: 0.6608 (m) cc_final: 0.6387 (t)
REVERT: A  864 GLU cc_start: 0.7789 (tt0) cc_final: 0.7488 (tp30)
REVERT: A  966 MET cc_start: 0.7429 (mmm) cc_final: 0.7186 (mmt)
REVERT: A  993 TYR cc_start: 0.6223 (t80) cc_final: 0.5467 (t80)
REVERT: A 1057 ARG cc_start: 0.6949 (tpt-90) cc_final: 0.6686 (mmm160)
REVERT: A 1088 GLN cc_start: 0.6431 (tt0) cc_final: 0.6191 (tt0)
REVERT: A 1123 LEU cc_start: 0.6189 (tp) cc_final: 0.5941 (mp)
REVERT: A 1280 MET cc_start: 0.6847 (mtm) cc_final: 0.6604 (mtm)
REVERT: A 1375 ASP cc_start: 0.6861 (p0) cc_final: 0.6554 (p0)
REVERT: A 1396 GLU cc_start: 0.7675 (mp0) cc_final: 0.6900 (pt0)
REVERT: A 1417 LYS cc_start: 0.7543 (mptt) cc_final: 0.7158 (mmmt)
REVERT: A 1465 ASP cc_start: 0.7282 (t70) cc_final: 0.7070 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2580
  time to fit residues: 64.8542
Evaluate side-chains
  128 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0570
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.7302

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

Flipped N/Q/H residues before XYZ refinement:
A 725 ASN
A1356 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.100961 restraints weight = 12726.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.47
r_work: 0.2983 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9892  Z= 0.224
  Angle     :  0.578   7.205  13450  Z= 0.299
  Chirality :  0.040   0.173   1574
  Planarity :  0.004   0.038   1654
  Dihedral  :  7.665  98.801   1541
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.02 %
    Favored  : 91.46 %
  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:  0.42 (0.23), residues: 1202
  helix:  1.39 (0.18), residues: 763
  sheet: -0.84 (0.53), residues: 77
  loop : -1.90 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 520 
 HIS   0.007   0.001   HIS A 382 
 PHE   0.009   0.001   PHE A 975 
 TYR   0.024   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A1495 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.122 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8255 (tt0)
REVERT: A  648 ASN cc_start: 0.8229 (t0) cc_final: 0.7829 (t0)
REVERT: A  742 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7768 (pt0)
REVERT: A  835 MET cc_start: 0.8830 (mmt) cc_final: 0.8266 (mmt)
REVERT: A  836 ASP cc_start: 0.7885 (m-30) cc_final: 0.7558 (t0)
REVERT: A 1238 GLN cc_start: 0.7486 (mt0) cc_final: 0.7148 (mm110)
REVERT: A 1375 ASP cc_start: 0.7366 (p0) cc_final: 0.6912 (p0)
REVERT: A 1393 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6119 (p90)
REVERT: A 1417 LYS cc_start: 0.8502 (mptt) cc_final: 0.8234 (mmmt)
REVERT: A 1465 ASP cc_start: 0.8141 (t70) cc_final: 0.7832 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 141
  average time/residue: 0.2417
  time to fit residues: 48.5463
Evaluate side-chains
  125 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
A 450 GLN
A1010 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.123602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.099394 restraints weight = 12619.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.83
r_work: 0.2936 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9892  Z= 0.207
  Angle     :  0.528   7.432  13450  Z= 0.270
  Chirality :  0.039   0.146   1574
  Planarity :  0.004   0.050   1654
  Dihedral  :  7.453  94.949   1541
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.82 %
    Favored  : 87.57 %
  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 (0.24), residues: 1202
  helix:  2.11 (0.18), residues: 759
  sheet: -0.60 (0.55), residues: 77
  loop : -1.57 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 520 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.011   0.001   PHE A 524 
 TYR   0.022   0.001   TYR A1032 
 ARG   0.003   0.000   ARG A1302 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8336 (tt0)
REVERT: A  648 ASN cc_start: 0.8165 (t0) cc_final: 0.7597 (t0)
REVERT: A  738 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7011 (pttp)
REVERT: A  742 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7824 (pt0)
REVERT: A  796 SER cc_start: 0.9034 (t) cc_final: 0.8808 (p)
REVERT: A  835 MET cc_start: 0.8892 (mmt) cc_final: 0.8421 (mmt)
REVERT: A  836 ASP cc_start: 0.7997 (m-30) cc_final: 0.7636 (t0)
REVERT: A 1278 GLN cc_start: 0.7939 (pp30) cc_final: 0.7442 (pp30)
REVERT: A 1293 GLU cc_start: 0.8072 (tt0) cc_final: 0.7843 (tt0)
REVERT: A 1302 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7318 (mtp-110)
REVERT: A 1393 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6131 (p90)
REVERT: A 1465 ASP cc_start: 0.8316 (t70) cc_final: 0.8064 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 129
  average time/residue: 0.2371
  time to fit residues: 43.5449
Evaluate side-chains
  125 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.123888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.099826 restraints weight = 12630.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.79
r_work: 0.2944 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9892  Z= 0.184
  Angle     :  0.497   7.315  13450  Z= 0.252
  Chirality :  0.038   0.134   1574
  Planarity :  0.004   0.058   1654
  Dihedral  :  7.277  94.688   1541
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.39 %
    Favored  : 87.10 %
  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:  1.62 (0.24), residues: 1202
  helix:  2.34 (0.19), residues: 761
  sheet: -0.41 (0.57), residues: 77
  loop : -1.43 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1197 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.002   0.000   ARG A 655 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.165 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8186 (tt0)
REVERT: A  648 ASN cc_start: 0.8076 (t0) cc_final: 0.7787 (m-40)
REVERT: A  738 LYS cc_start: 0.8218 (ttmt) cc_final: 0.6784 (pttp)
REVERT: A  742 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7633 (pt0)
REVERT: A  796 SER cc_start: 0.9022 (t) cc_final: 0.8814 (p)
REVERT: A  835 MET cc_start: 0.8736 (mmt) cc_final: 0.8428 (mmp)
REVERT: A  836 ASP cc_start: 0.7959 (m-30) cc_final: 0.7534 (t0)
REVERT: A 1278 GLN cc_start: 0.7993 (pp30) cc_final: 0.7612 (pp30)
REVERT: A 1293 GLU cc_start: 0.8005 (tt0) cc_final: 0.7740 (tt0)
REVERT: A 1302 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7091 (mtp180)
REVERT: A 1393 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6019 (p90)
REVERT: A 1465 ASP cc_start: 0.8218 (t70) cc_final: 0.7993 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 130
  average time/residue: 0.2127
  time to fit residues: 40.2005
Evaluate side-chains
  126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1302 ARG
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0470
   chunk 71 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 = 0.3358 r_free = 0.3358 target = 0.122701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.100868 restraints weight = 12645.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.50
r_work: 0.2976 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9892  Z= 0.188
  Angle     :  0.498   7.290  13450  Z= 0.253
  Chirality :  0.038   0.192   1574
  Planarity :  0.004   0.062   1654
  Dihedral  :  7.177  94.672   1541
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.33 %
    Favored  : 85.77 %
  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:  1.71 (0.24), residues: 1202
  helix:  2.39 (0.19), residues: 762
  sheet: -0.40 (0.57), residues: 76
  loop : -1.35 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1197 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.001   0.000   ARG A1074 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8188 (tt0)
REVERT: A  648 ASN cc_start: 0.8094 (t0) cc_final: 0.7808 (m-40)
REVERT: A  738 LYS cc_start: 0.8283 (ttmt) cc_final: 0.6862 (pttp)
REVERT: A  742 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7670 (pt0)
REVERT: A  824 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8337 (pp)
REVERT: A  835 MET cc_start: 0.8819 (mmt) cc_final: 0.8508 (mmp)
REVERT: A  836 ASP cc_start: 0.7916 (m-30) cc_final: 0.7517 (t0)
REVERT: A 1130 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7817 (mmp-170)
REVERT: A 1293 GLU cc_start: 0.7957 (tt0) cc_final: 0.7725 (tt0)
REVERT: A 1302 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7161 (mtp180)
REVERT: A 1380 SER cc_start: 0.9063 (t) cc_final: 0.8837 (p)
REVERT: A 1393 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6114 (p90)
REVERT: A 1465 ASP cc_start: 0.8262 (t70) cc_final: 0.8019 (t0)
REVERT: A 1526 ASP cc_start: 0.7945 (m-30) cc_final: 0.7736 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 128
  average time/residue: 0.2327
  time to fit residues: 42.2761
Evaluate side-chains
  124 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 2.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1130 ARG
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1302 ARG
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Chi-restraints excluded: chain A residue 1481 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 108 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 114 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.102436 restraints weight = 12639.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.47
r_work: 0.2982 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9892  Z= 0.189
  Angle     :  0.496   7.161  13450  Z= 0.252
  Chirality :  0.038   0.161   1574
  Planarity :  0.004   0.062   1654
  Dihedral  :  7.052  92.763   1541
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.52 %
    Favored  : 85.39 %
  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:  1.78 (0.24), residues: 1202
  helix:  2.44 (0.19), residues: 762
  sheet: -0.34 (0.58), residues: 76
  loop : -1.32 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1197 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.003   0.000   ARG A 233 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
REVERT: A  623 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8207 (tt0)
REVERT: A  648 ASN cc_start: 0.8072 (t0) cc_final: 0.7776 (m-40)
REVERT: A  738 LYS cc_start: 0.8292 (ttmt) cc_final: 0.6938 (pttp)
REVERT: A  742 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7734 (pt0)
REVERT: A  824 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8328 (pp)
REVERT: A  835 MET cc_start: 0.8812 (mmt) cc_final: 0.8409 (mmt)
REVERT: A  836 ASP cc_start: 0.7887 (m-30) cc_final: 0.7516 (t0)
REVERT: A 1130 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (mmp-170)
REVERT: A 1293 GLU cc_start: 0.7976 (tt0) cc_final: 0.7745 (tt0)
REVERT: A 1393 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5956 (p90)
REVERT: A 1465 ASP cc_start: 0.8273 (t70) cc_final: 0.8029 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2295
  time to fit residues: 41.5644
Evaluate side-chains
  127 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1130 ARG
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1278 GLN
Chi-restraints excluded: chain A residue 1302 ARG
Chi-restraints excluded: chain A residue 1337 LEU
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Chi-restraints excluded: chain A residue 1481 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0070
   chunk 109 optimal weight:    0.0030
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.4208

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

Flipped N/Q/H residues before XYZ refinement:
A1515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.102101 restraints weight = 12615.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.79
r_work: 0.2969 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9892  Z= 0.150
  Angle     :  0.480   7.065  13450  Z= 0.244
  Chirality :  0.037   0.151   1574
  Planarity :  0.004   0.061   1654
  Dihedral  :  6.886  87.276   1541
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.66 %
    Favored  : 84.63 %
  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:  1.99 (0.24), residues: 1202
  helix:  2.62 (0.19), residues: 761
  sheet: -0.28 (0.58), residues: 76
  loop : -1.25 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1197 
 HIS   0.008   0.001   HIS A 382 
 PHE   0.008   0.001   PHE A 524 
 TYR   0.020   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 655 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8138 (tt0)
REVERT: A  648 ASN cc_start: 0.8014 (t0) cc_final: 0.7702 (m-40)
REVERT: A  738 LYS cc_start: 0.8181 (ttmt) cc_final: 0.6770 (pttp)
REVERT: A  742 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7591 (pt0)
REVERT: A  824 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8164 (pp)
REVERT: A  835 MET cc_start: 0.8706 (mmt) cc_final: 0.8290 (mmt)
REVERT: A  836 ASP cc_start: 0.7961 (m-30) cc_final: 0.7554 (t0)
REVERT: A 1034 MET cc_start: 0.8357 (tpp) cc_final: 0.8135 (mmm)
REVERT: A 1130 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7748 (mmp-170)
REVERT: A 1293 GLU cc_start: 0.8022 (tt0) cc_final: 0.7772 (tt0)
REVERT: A 1393 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5867 (p90)
REVERT: A 1465 ASP cc_start: 0.8214 (t70) cc_final: 0.8000 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 124
  average time/residue: 0.2126
  time to fit residues: 37.9772
Evaluate side-chains
  122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1130 ARG
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1278 GLN
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Chi-restraints excluded: chain A residue 1481 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 118 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.102505 restraints weight = 12581.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.76
r_work: 0.2945 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9892  Z= 0.208
  Angle     :  0.503   7.055  13450  Z= 0.256
  Chirality :  0.038   0.159   1574
  Planarity :  0.004   0.061   1654
  Dihedral  :  6.871  82.500   1541
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.04 %
    Favored  : 84.44 %
  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:  1.81 (0.24), residues: 1202
  helix:  2.44 (0.19), residues: 768
  sheet: -0.24 (0.58), residues: 76
  loop : -1.35 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1245 
 HIS   0.012   0.001   HIS A 382 
 PHE   0.011   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 655 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 1.263 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8141 (tt0)
REVERT: A  648 ASN cc_start: 0.8026 (t0) cc_final: 0.7706 (m-40)
REVERT: A  738 LYS cc_start: 0.8221 (ttmt) cc_final: 0.6857 (pttp)
REVERT: A  742 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7623 (pt0)
REVERT: A  824 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8274 (pp)
REVERT: A  835 MET cc_start: 0.8763 (mmt) cc_final: 0.8323 (mmt)
REVERT: A  836 ASP cc_start: 0.7968 (m-30) cc_final: 0.7555 (t0)
REVERT: A  966 MET cc_start: 0.8096 (mmt) cc_final: 0.7595 (mmt)
REVERT: A 1034 MET cc_start: 0.8413 (tpp) cc_final: 0.8182 (mmm)
REVERT: A 1293 GLU cc_start: 0.7982 (tt0) cc_final: 0.7756 (tt0)
REVERT: A 1302 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7596 (mtp180)
REVERT: A 1393 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6031 (p90)
REVERT: A 1465 ASP cc_start: 0.8261 (t70) cc_final: 0.8039 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 115
  average time/residue: 0.2206
  time to fit residues: 36.5201
Evaluate side-chains
  117 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1278 GLN
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Chi-restraints excluded: chain A residue 1481 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 590 ASN
A1515 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100596 restraints weight = 12661.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.53
r_work: 0.2967 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9892  Z= 0.206
  Angle     :  0.505   6.760  13450  Z= 0.257
  Chirality :  0.038   0.156   1574
  Planarity :  0.004   0.061   1654
  Dihedral  :  6.735  77.381   1541
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.85 %
    Favored  : 84.44 %
  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:  1.76 (0.24), residues: 1202
  helix:  2.40 (0.18), residues: 768
  sheet: -0.23 (0.57), residues: 76
  loop : -1.34 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1197 
 HIS   0.012   0.001   HIS A 382 
 PHE   0.010   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 655 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.208 
Fit side-chains
REVERT: A  623 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8177 (tt0)
REVERT: A  648 ASN cc_start: 0.8064 (t0) cc_final: 0.7754 (m-40)
REVERT: A  738 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7115 (pttp)
REVERT: A  824 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8306 (pp)
REVERT: A  835 MET cc_start: 0.8833 (mmt) cc_final: 0.8377 (mmt)
REVERT: A  836 ASP cc_start: 0.7960 (m-30) cc_final: 0.7600 (t0)
REVERT: A  966 MET cc_start: 0.8093 (mmt) cc_final: 0.7641 (mmt)
REVERT: A 1034 MET cc_start: 0.8383 (tpp) cc_final: 0.8136 (mmm)
REVERT: A 1249 MET cc_start: 0.8359 (tpp) cc_final: 0.8128 (mmt)
REVERT: A 1293 GLU cc_start: 0.7963 (tt0) cc_final: 0.7679 (tt0)
REVERT: A 1393 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5956 (p90)
REVERT: A 1465 ASP cc_start: 0.8287 (t70) cc_final: 0.8037 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 118
  average time/residue: 0.2243
  time to fit residues: 38.2089
Evaluate side-chains
  117 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1278 GLN
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Chi-restraints excluded: chain A residue 1481 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0030
   chunk 108 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0030
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.2980
   overall best weight:    0.3400

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

Flipped N/Q/H residues before XYZ refinement:
A1515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.126214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.103702 restraints weight = 12642.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.60
r_work: 0.3015 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9892  Z= 0.143
  Angle     :  0.477   6.260  13450  Z= 0.243
  Chirality :  0.037   0.148   1574
  Planarity :  0.004   0.060   1654
  Dihedral  :  6.370  80.508   1541
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.33 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.25), residues: 1202
  helix:  2.68 (0.19), residues: 763
  sheet: -0.06 (0.58), residues: 76
  loop : -1.25 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1197 
 HIS   0.008   0.001   HIS A 382 
 PHE   0.008   0.001   PHE A1030 
 TYR   0.020   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 655 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A  648 ASN cc_start: 0.8037 (t0) cc_final: 0.7738 (m-40)
REVERT: A  738 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7109 (pttp)
REVERT: A  824 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8111 (pp)
REVERT: A  835 MET cc_start: 0.8768 (mmt) cc_final: 0.8324 (mmt)
REVERT: A  966 MET cc_start: 0.8120 (mmt) cc_final: 0.7664 (mmt)
REVERT: A 1034 MET cc_start: 0.8367 (tpp) cc_final: 0.8138 (mmm)
REVERT: A 1249 MET cc_start: 0.8342 (tpp) cc_final: 0.8122 (mmt)
REVERT: A 1293 GLU cc_start: 0.8081 (tt0) cc_final: 0.7854 (tt0)
REVERT: A 1393 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5936 (p90)
REVERT: A 1465 ASP cc_start: 0.8261 (t70) cc_final: 0.8032 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 119
  average time/residue: 0.2248
  time to fit residues: 38.5577
Evaluate side-chains
  115 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1278 GLN
Chi-restraints excluded: chain A residue 1357 ILE
Chi-restraints excluded: chain A residue 1393 TYR
Chi-restraints excluded: chain A residue 1429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 74 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0070
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
A1515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.103504 restraints weight = 12612.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.51
r_work: 0.3003 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9892  Z= 0.169
  Angle     :  0.486   6.192  13450  Z= 0.246
  Chirality :  0.038   0.150   1574
  Planarity :  0.004   0.061   1654
  Dihedral  :  6.288  78.875   1541
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.42 %
    Favored  : 84.25 %
  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:  2.01 (0.25), residues: 1202
  helix:  2.60 (0.19), residues: 768
  sheet: -0.00 (0.58), residues: 76
  loop : -1.29 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1197 
 HIS   0.009   0.001   HIS A 382 
 PHE   0.009   0.001   PHE A 524 
 TYR   0.021   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 655 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4730.74 seconds
wall clock time: 84 minutes 52.88 seconds (5092.88 seconds total)