Starting phenix.real_space_refine
on Thu Sep 18 06:58:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yii_39320/09_2025/8yii_39320.cif"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.003
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     106      5.49       5
     Mg      5      5.21       5
     S      67      5.16       5
     C    9083      2.51       5
     N    2543      2.21       5
     O    3051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14855
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 12470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1541, 12470
          Classifications: {'peptide': 1541}
          Link IDs: {'PTRANS': 63, 'TRANS': 1477}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 143
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "C"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 2210
          Classifications: {'RNA': 104}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 49, 'rna3p_pyr': 52}
          Link IDs: {'rna2p': 3, 'rna3p': 100}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 32
          Unusual residues: {' MG': 5, 'ADP': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 3.29, per 1000 atoms: 0.22
  Number of scatterers: 14855
  At special positions: 0
  Unit cell: (92.88, 95.04, 177.12, 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      67     16.00
     P     106     15.00
     Mg      5     11.99
     O    3051      8.00
     N    2543      7.00
     C    9083      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: 1.33
  Conformation dependent library (CDL) restraints added in 503.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2976

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 11 sheets defined
      54.1% alpha, 10.8% beta
      40 base pairs and 60 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 22
      removed outlier: 3.851A  pdb=" N   LYS A  21 " --> pdb=" O   ASP A  17 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER A  22 " --> pdb=" O   HIS A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 45
    Processing helix  chain 'A' and resid 46 through 49
      removed outlier: 3.665A  pdb=" N   PHE A  49 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 46 through 49'
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 89 through 97
      removed outlier: 6.291A  pdb=" N   VAL A  94 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP A  95 " --> pdb=" O   GLN A  92 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ASP A  96 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 4.234A  pdb=" N   GLU A 105 " --> pdb=" O   MET A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 125
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 141 through 144
    Processing helix  chain 'A' and resid 148 through 160
    Processing helix  chain 'A' and resid 183 through 195
      removed outlier: 3.696A  pdb=" N   LYS A 187 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 213
      removed outlier: 3.650A  pdb=" N   ASN A 210 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 252
    Processing helix  chain 'A' and resid 271 through 292
    Processing helix  chain 'A' and resid 292 through 313
      removed outlier: 3.725A  pdb=" N   ILE A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 346
      removed outlier: 3.878A  pdb=" N   MET A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 363
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 394 through 411
      removed outlier: 3.674A  pdb=" N   CYS A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 452
    Processing helix  chain 'A' and resid 462 through 466
      removed outlier: 3.886A  pdb=" N   GLU A 466 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.720A  pdb=" N   ALA A 495 " --> pdb=" O   SER A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 535
      removed outlier: 3.623A  pdb=" N   ALA A 529 " --> pdb=" O   HIS A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 567 through 569
      No H-bonds generated for 'chain 'A' and resid 567 through 569'
    Processing helix  chain 'A' and resid 570 through 582
      removed outlier: 3.575A  pdb=" N   THR A 581 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 582 " --> pdb=" O   TYR A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 606
      removed outlier: 3.717A  pdb=" N   ASP A 603 " --> pdb=" O   GLU A 599 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ARG A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
      removed outlier: 3.585A  pdb=" N   ALA A 610 " --> pdb=" O   GLY A 607 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   GLY A 612 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 656
    Processing helix  chain 'A' and resid 672 through 677
    Processing helix  chain 'A' and resid 680 through 687
      removed outlier: 3.506A  pdb=" N   TRP A 683 " --> pdb=" O   PHE A 680 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 685 " --> pdb=" O   HIS A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 749
      removed outlier: 3.718A  pdb=" N   GLN A 749 " --> pdb=" O   TYR A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 810
      removed outlier: 3.586A  pdb=" N   LEU A 796 " --> pdb=" O   ASN A 792 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE A 807 " --> pdb=" O   HIS A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 862 through 869
    Processing helix  chain 'A' and resid 873 through 877
      removed outlier: 4.218A  pdb=" N   PHE A 877 " --> pdb=" O   PRO A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 926
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 3.648A  pdb=" N   GLY A 957 " --> pdb=" O   HIS A 954 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS A 958 " --> pdb=" O   ASN A 955 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 954 through 958'
    Processing helix  chain 'A' and resid 960 through 964
      removed outlier: 3.645A  pdb=" N   LYS A 964 " --> pdb=" O   ALA A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 974
      No H-bonds generated for 'chain 'A' and resid 972 through 974'
    Processing helix  chain 'A' and resid 983 through 991
      removed outlier: 4.115A  pdb=" N   PHE A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 1016
    Processing helix  chain 'A' and resid 1020 through 1024
      removed outlier: 3.585A  pdb=" N   ASN A1024 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1174 through 1182
    Processing helix  chain 'A' and resid 1190 through 1199
    Processing helix  chain 'A' and resid 1200 through 1204
    Processing helix  chain 'A' and resid 1209 through 1232
      removed outlier: 3.978A  pdb=" N   ILE A1214 " --> pdb=" O   GLU A1210 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU A1215 " --> pdb=" O   ARG A1211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1248
      removed outlier: 3.826A  pdb=" N   LYS A1246 " --> pdb=" O   GLU A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1260
    Processing helix  chain 'A' and resid 1261 through 1266
      removed outlier: 4.090A  pdb=" N   LYS A1264 " --> pdb=" O   ASP A1261 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A1266 " --> pdb=" O   PRO A1263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1277
    Processing helix  chain 'A' and resid 1285 through 1295
    Processing helix  chain 'A' and resid 1303 through 1309
    Processing helix  chain 'A' and resid 1313 through 1319
    Processing helix  chain 'A' and resid 1324 through 1339
      removed outlier: 4.102A  pdb=" N   GLY A1334 " --> pdb=" O   ARG A1330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1382
    Processing helix  chain 'A' and resid 1383 through 1393
    Processing helix  chain 'A' and resid 1422 through 1430
      removed outlier: 3.563A  pdb=" N   ILE A1426 " --> pdb=" O   ASN A1422 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   ASP A1427 " --> pdb=" O   THR A1423 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY A1428 " --> pdb=" O   THR A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1441
      removed outlier: 3.611A  pdb=" N   LEU A1436 " --> pdb=" O   ASN A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1455
      removed outlier: 4.280A  pdb=" N   LEU A1450 " --> pdb=" O   ASP A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1461 through 1466
    Processing helix  chain 'A' and resid 1467 through 1491
      removed outlier: 4.625A  pdb=" N   LEU A1471 " --> pdb=" O   SER A1467 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE A1473 " --> pdb=" O   GLN A1469 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE A1474 " --> pdb=" O   GLU A1470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1495 through 1507
    Processing helix  chain 'A' and resid 1508 through 1519
    Processing helix  chain 'A' and resid 1520 through 1525
      removed outlier: 3.762A  pdb=" N   PHE A1523 " --> pdb=" O   ARG A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1547
      removed outlier: 3.902A  pdb=" N   ILE A1535 " --> pdb=" O   LYS A1531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1610 through 1628
      removed outlier: 3.573A  pdb=" N   ASP A1614 " --> pdb=" O   LYS A1610 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   CYS A1627 " --> pdb=" O   VAL A1623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1629 through 1651
      Proline residue:  A1643  - end of helix
    Processing helix  chain 'A' and resid 1655 through 1663
    Processing helix  chain 'A' and resid 1701 through 1719
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.275A  pdb=" N   SER A 134 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL A 136 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   LEU A 171 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ILE A 138 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ARG A  59 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ILE A 137 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LEU A  61 " --> pdb=" O   ILE A 137 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ASP A 139 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   MET A  63 " --> pdb=" O   ASP A 139 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ALA A  60 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   GLY A 114 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   PHE A  62 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   GLY A  86 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   THR A 115 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   TYR A  88 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424
      removed outlier: 6.060A  pdb=" N   VAL A 476 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   PHE A 505 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ILE A 478 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 9.104A  pdb=" N   ALA A 507 " --> pdb=" O   ILE A 478 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261
      removed outlier: 4.455A  pdb=" N   ARG A 260 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559
      removed outlier: 3.586A  pdb=" N   PHE A 558 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596
      removed outlier: 3.684A  pdb=" N   ILE A 630 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706
    Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772
    Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772
      removed outlier: 4.674A  pdb=" N   TYR A 754 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   GLN A 841 " --> pdb=" O   GLY A 837 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820
    Processing sheet with id=AB1, first strand: chain 'A' and resid 970 through 971
      removed outlier: 3.520A  pdb=" N   ILE A 940 " --> pdb=" O   LEU A 971 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ARG A 943 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   VAL A 895 " --> pdb=" O   ARG A 943 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LYS A 880 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 881 " --> pdb=" O   PHE A 979 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1680 through 1688
      removed outlier: 3.529A  pdb=" N   VAL A1695 " --> pdb=" O   CYS A1684 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE A1686 " --> pdb=" O   ILE A1693 " (cutoff:3.500A)

    610 hydrogen bonds defined for protein.
    1737 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      102 hydrogen bonds
      188 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      60 stacking parallelities
  Total time for adding SS restraints: 3.36

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4334
        1.34 -     1.46: 2997
        1.46 -     1.57: 7731
        1.57 -     1.69: 212
        1.69 -     1.81: 105
  Bond restraints: 15379
  Sorted by residual:
  bond pdb=" P     G C   1 "
       pdb=" OP3   G C   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.605 -0.125 2.00e-02 2.50e+03 3.88e+01
  bond pdb=" CB  PRO A 872 "
       pdb=" CG  PRO A 872 "
    ideal  model  delta    sigma   weight residual
    1.492  1.641 -0.149 5.00e-02 4.00e+02 8.84e+00
  bond pdb=" N   PRO A 872 "
       pdb=" CA  PRO A 872 "
    ideal  model  delta    sigma   weight residual
    1.472  1.454  0.018 1.17e-02 7.31e+03 2.25e+00
  bond pdb=" CA  TYR A1037 "
       pdb=" C   TYR A1037 "
    ideal  model  delta    sigma   weight residual
    1.522  1.541 -0.019 1.38e-02 5.25e+03 1.85e+00
  bond pdb=" C   LYS A1667 "
       pdb=" O   LYS A1667 "
    ideal  model  delta    sigma   weight residual
    1.242  1.226  0.016 1.16e-02 7.43e+03 1.84e+00
  ... (remaining 15374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 21021
        2.26 -     4.53: 243
        4.53 -     6.79: 43
        6.79 -     9.05: 3
        9.05 -    11.32: 2
  Bond angle restraints: 21312
  Sorted by residual:
  angle pdb=" CA  PRO A 872 "
        pdb=" N   PRO A 872 "
        pdb=" CD  PRO A 872 "
      ideal   model   delta    sigma   weight residual
     112.00  100.68   11.32 1.40e+00 5.10e-01 6.54e+01
  angle pdb=" CA  TYR A 918 "
        pdb=" CB  TYR A 918 "
        pdb=" CG  TYR A 918 "
      ideal   model   delta    sigma   weight residual
     113.90  121.08   -7.18 1.80e+00 3.09e-01 1.59e+01
  angle pdb=" CB  MET A 922 "
        pdb=" CG  MET A 922 "
        pdb=" SD  MET A 922 "
      ideal   model   delta    sigma   weight residual
     112.70  101.46   11.24 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" N   VAL A1206 "
        pdb=" CA  VAL A1206 "
        pdb=" C   VAL A1206 "
      ideal   model   delta    sigma   weight residual
     112.29  109.17    3.12 9.40e-01 1.13e+00 1.10e+01
  angle pdb=" N   PRO A 872 "
        pdb=" CD  PRO A 872 "
        pdb=" CG  PRO A 872 "
      ideal   model   delta    sigma   weight residual
     103.20   98.47    4.73 1.50e+00 4.44e-01 9.94e+00
  ... (remaining 21307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.80: 8891
       32.80 -    65.59: 516
       65.59 -    98.39: 64
       98.39 -   131.18: 2
      131.18 -   163.98: 1
  Dihedral angle restraints: 9474
    sinusoidal: 4886
      harmonic: 4588
  Sorted by residual:
  dihedral pdb=" O4'   U C 103 "
           pdb=" C1'   U C 103 "
           pdb=" N1    U C 103 "
           pdb=" C2    U C 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   35.98 -163.98     1      1.70e+01 3.46e-03 6.51e+01
  dihedral pdb=" C5' ADP A1801 "
           pdb=" O5' ADP A1801 "
           pdb=" PA  ADP A1801 "
           pdb=" O2A ADP A1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -160.78  100.78     1      2.00e+01 2.50e-03 2.85e+01
  dihedral pdb=" O1B ADP A1801 "
           pdb=" O3A ADP A1801 "
           pdb=" PB  ADP A1801 "
           pdb=" PA  ADP A1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -157.35   97.34     1      2.00e+01 2.50e-03 2.71e+01
  ... (remaining 9471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1878
       0.038 -    0.076: 441
       0.076 -    0.114: 132
       0.114 -    0.151: 22
       0.151 -    0.189: 4
  Chirality restraints: 2477
  Sorted by residual:
  chirality pdb=" CA  PRO A 872 "
            pdb=" N   PRO A 872 "
            pdb=" C   PRO A 872 "
            pdb=" CB  PRO A 872 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.95e-01
  chirality pdb=" C3'   G C  97 "
            pdb=" C4'   G C  97 "
            pdb=" O3'   G C  97 "
            pdb=" C2'   G C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.29   -0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CB  ILE A1301 "
            pdb=" CA  ILE A1301 "
            pdb=" CG1 ILE A1301 "
            pdb=" CG2 ILE A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.21e-01
  ... (remaining 2474 not shown)

  Planarity restraints: 2337
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 871 "    0.075 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A 872 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 872 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 872 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 768 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO A 769 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 769 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 769 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 148 "    0.028 5.00e-02 4.00e+02   4.18e-02 2.79e+00
        pdb=" N   PRO A 149 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "    0.023 5.00e-02 4.00e+02
  ... (remaining 2334 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 124
        2.53 -     3.13: 11496
        3.13 -     3.72: 25914
        3.72 -     4.31: 34468
        4.31 -     4.90: 54169
  Nonbonded interactions: 126171
  Sorted by model distance:
  nonbonded pdb=" OP1   G C  23 "
            pdb="MG    MG A1803 "
     model   vdw
     1.943 2.170
  nonbonded pdb=" OE1 GLU A1213 "
            pdb="MG    MG A1805 "
     model   vdw
     1.988 2.170
  nonbonded pdb=" OP1   U C  84 "
            pdb="MG    MG A1802 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" OE1 GLU A1210 "
            pdb="MG    MG A1805 "
     model   vdw
     2.030 2.170
  nonbonded pdb=" OE2 GLU A1617 "
            pdb="MG    MG A1803 "
     model   vdw
     2.044 2.170
  ... (remaining 126166 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:                  0.010
  Normalize map: mean=0, sd=1:             0.900
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.530
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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      :  0.003   0.149  15379  Z= 0.146
  Angle     :  0.640  11.318  21312  Z= 0.352
  Chirality :  0.037   0.189   2477
  Planarity :  0.004   0.105   2337
  Dihedral  : 18.822 163.978   6498
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.39 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 16.64 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.22), residues: 1549
  helix:  0.72 (0.19), residues: 746
  sheet: -0.37 (0.38), residues: 187
  loop : -0.67 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1658 
 TYR   0.027   0.001   TYR A1037 
 PHE   0.022   0.001   PHE A 589 
 TRP   0.016   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (15379)
  covalent geometry    : angle       0.63957 (21312)
  hydrogen bonds       : bond        0.15258 (  702)
  hydrogen bonds       : angle       6.47148 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 THR cc_start: 0.6991 (p) cc_final: 0.6494 (t)
REVERT: A  847 GLU cc_start: 0.8330 (mp0) cc_final: 0.8117 (tp30)
REVERT: A 1246 LYS cc_start: 0.8566 (mppt) cc_final: 0.8265 (mmmt)
REVERT: A 1389 MET cc_start: 0.7996 (tpp) cc_final: 0.7719 (mmm)
  outliers start: 7
  outliers final: 2
  residues processed: 147
  average time/residue: 0.1315
  time to fit residues: 28.7216
Evaluate side-chains
  127 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0070
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0010
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    0.4604

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
A 287 GLN
A 801 GLN
A 841 GLN
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN
A1704 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.116157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.081567 restraints weight = 31356.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.88
r_work: 0.3135 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  15379  Z= 0.113
  Angle     :  0.559   8.736  21312  Z= 0.289
  Chirality :  0.038   0.222   2477
  Planarity :  0.004   0.041   2337
  Dihedral  : 17.183 164.372   3358
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.07 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.00 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.21), residues: 1549
  helix:  0.87 (0.19), residues: 751
  sheet: -0.35 (0.37), residues: 179
  loop : -0.69 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 900 
 TYR   0.018   0.001   TYR A1232 
 PHE   0.016   0.001   PHE A1473 
 TRP   0.016   0.002   TRP A 814 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (15379)
  covalent geometry    : angle       0.55871 (21312)
  hydrogen bonds       : bond        0.04358 (  702)
  hydrogen bonds       : angle       4.83576 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 VAL cc_start: 0.8688 (m) cc_final: 0.8445 (m)
REVERT: A  744 MET cc_start: 0.8795 (tpp) cc_final: 0.8496 (mmt)
REVERT: A  847 GLU cc_start: 0.8515 (mp0) cc_final: 0.8225 (tp30)
REVERT: A  873 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.7510 (mmp80)
REVERT: A  918 TYR cc_start: 0.7573 (t80) cc_final: 0.7258 (t80)
REVERT: A  934 HIS cc_start: 0.7199 (t-90) cc_final: 0.6611 (t-90)
REVERT: A 1246 LYS cc_start: 0.8554 (mppt) cc_final: 0.8308 (mmmt)
REVERT: A 1674 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.5727 (mm)
REVERT: A 1681 MET cc_start: 0.5814 (ppp) cc_final: 0.5373 (tmm)
REVERT: A 1704 GLN cc_start: 0.8426 (tp40) cc_final: 0.8163 (tp-100)
  outliers start: 31
  outliers final: 12
  residues processed: 157
  average time/residue: 0.1092
  time to fit residues: 25.9955
Evaluate side-chains
  126 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1674 ILE
Chi-restraints excluded: chain A residue 1688 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 135 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 109 ASN
A 562 ASN
A 800 HIS
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1656 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.114693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.084907 restraints weight = 31583.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.50
r_work: 0.3105 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  15379  Z= 0.129
  Angle     :  0.551   7.642  21312  Z= 0.282
  Chirality :  0.038   0.231   2477
  Planarity :  0.004   0.043   2337
  Dihedral  : 17.042 163.473   3358
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.94 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.43 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.21), residues: 1549
  helix:  0.92 (0.19), residues: 746
  sheet: -0.53 (0.36), residues: 185
  loop : -0.70 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 627 
 TYR   0.016   0.001   TYR A1232 
 PHE   0.018   0.001   PHE A1473 
 TRP   0.011   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (15379)
  covalent geometry    : angle       0.55141 (21312)
  hydrogen bonds       : bond        0.04115 (  702)
  hydrogen bonds       : angle       4.60810 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 LEU cc_start: 0.8419 (tt) cc_final: 0.8074 (mt)
REVERT: A  847 GLU cc_start: 0.8470 (mp0) cc_final: 0.8241 (tp30)
REVERT: A  934 HIS cc_start: 0.7354 (t-90) cc_final: 0.6994 (t-90)
REVERT: A 1037 TYR cc_start: 0.6558 (t80) cc_final: 0.6085 (t80)
REVERT: A 1389 MET cc_start: 0.7890 (mmm) cc_final: 0.7223 (tpp)
REVERT: A 1674 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.5557 (mm)
REVERT: A 1681 MET cc_start: 0.5673 (ppp) cc_final: 0.5268 (tmm)
  outliers start: 31
  outliers final: 19
  residues processed: 141
  average time/residue: 0.1107
  time to fit residues: 24.5376
Evaluate side-chains
  129 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1674 ILE
Chi-restraints excluded: chain A residue 1688 CYS
Chi-restraints excluded: chain A residue 1717 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 151 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 143 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.113155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.081540 restraints weight = 31682.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.77
r_work: 0.3052 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15379  Z= 0.164
  Angle     :  0.572   7.055  21312  Z= 0.294
  Chirality :  0.040   0.239   2477
  Planarity :  0.004   0.044   2337
  Dihedral  : 16.999 160.620   3358
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.39 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.00 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.21), residues: 1549
  helix:  0.81 (0.19), residues: 749
  sheet: -0.57 (0.36), residues: 191
  loop : -0.74 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 866 
 TYR   0.017   0.002   TYR A1232 
 PHE   0.019   0.002   PHE A1473 
 TRP   0.011   0.001   TRP A1634 
 HIS   0.004   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (15379)
  covalent geometry    : angle       0.57229 (21312)
  hydrogen bonds       : bond        0.04242 (  702)
  hydrogen bonds       : angle       4.58863 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 115
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 LEU cc_start: 0.8422 (tt) cc_final: 0.8082 (mt)
REVERT: A  934 HIS cc_start: 0.7464 (t-90) cc_final: 0.7043 (t-90)
REVERT: A 1037 TYR cc_start: 0.6638 (t80) cc_final: 0.6127 (t80)
REVERT: A 1417 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7112 (mpp)
REVERT: A 1674 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.5724 (mm)
REVERT: A 1681 MET cc_start: 0.5911 (ppp) cc_final: 0.5398 (tmm)
  outliers start: 42
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1089
  time to fit residues: 24.5976
Evaluate side-chains
  137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  442 TRP
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Chi-restraints excluded: chain A residue 1688 CYS
Chi-restraints excluded: chain A residue 1717 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 152 optimal weight:    4.9990
   chunk 154 optimal weight:   10.0000
   chunk 161 optimal weight:    5.9990
   chunk 148 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0980
   chunk 48 optimal weight:    1.9990
   chunk 143 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 163 optimal weight:    4.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.114935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.080398 restraints weight = 31656.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.86
r_work: 0.3107 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  15379  Z= 0.110
  Angle     :  0.532   6.922  21312  Z= 0.271
  Chirality :  0.038   0.230   2477
  Planarity :  0.003   0.045   2337
  Dihedral  : 17.007 162.739   3358
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.50 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.21), residues: 1549
  helix:  0.95 (0.19), residues: 749
  sheet: -0.58 (0.36), residues: 186
  loop : -0.73 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 671 
 TYR   0.015   0.001   TYR A1232 
 PHE   0.015   0.001   PHE A1473 
 TRP   0.012   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (15379)
  covalent geometry    : angle       0.53216 (21312)
  hydrogen bonds       : bond        0.03764 (  702)
  hydrogen bonds       : angle       4.42663 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 VAL cc_start: 0.8635 (m) cc_final: 0.8419 (m)
REVERT: A  504 LEU cc_start: 0.8440 (tt) cc_final: 0.8206 (mt)
REVERT: A  900 ARG cc_start: 0.7412 (mtt90) cc_final: 0.6431 (mpt90)
REVERT: A  934 HIS cc_start: 0.7438 (t-90) cc_final: 0.6978 (t-90)
REVERT: A 1037 TYR cc_start: 0.6526 (t80) cc_final: 0.6017 (t80)
REVERT: A 1417 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6874 (mpp)
REVERT: A 1604 THR cc_start: 0.4338 (OUTLIER) cc_final: 0.4039 (m)
REVERT: A 1674 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5556 (mm)
REVERT: A 1681 MET cc_start: 0.6082 (ppp) cc_final: 0.5594 (tmm)
  outliers start: 38
  outliers final: 20
  residues processed: 148
  average time/residue: 0.1161
  time to fit residues: 26.1626
Evaluate side-chains
  136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1462 ASN
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 150 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0370
   chunk 94 optimal weight:    0.0970
   overall best weight:    1.2060

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

Flipped N/Q/H residues before XYZ refinement:
A 800 HIS
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.114297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.079426 restraints weight = 31407.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.86
r_work: 0.3091 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  15379  Z= 0.133
  Angle     :  0.543   7.128  21312  Z= 0.277
  Chirality :  0.038   0.234   2477
  Planarity :  0.003   0.044   2337
  Dihedral  : 16.974 162.424   3358
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.64 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.21), residues: 1549
  helix:  0.91 (0.19), residues: 750
  sheet: -0.57 (0.36), residues: 186
  loop : -0.75 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 671 
 TYR   0.016   0.001   TYR A1232 
 PHE   0.017   0.001   PHE A1473 
 TRP   0.012   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (15379)
  covalent geometry    : angle       0.54266 (21312)
  hydrogen bonds       : bond        0.03837 (  702)
  hydrogen bonds       : angle       4.41364 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  900 ARG cc_start: 0.7414 (mtt90) cc_final: 0.6443 (mpt90)
REVERT: A  934 HIS cc_start: 0.7533 (t-90) cc_final: 0.6986 (t-90)
REVERT: A  939 MET cc_start: 0.5427 (tpp) cc_final: 0.4800 (tpp)
REVERT: A 1037 TYR cc_start: 0.6593 (t80) cc_final: 0.6099 (t80)
REVERT: A 1417 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6683 (mpp)
REVERT: A 1604 THR cc_start: 0.4696 (OUTLIER) cc_final: 0.4412 (m)
REVERT: A 1674 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.5671 (mm)
REVERT: A 1681 MET cc_start: 0.6073 (ppp) cc_final: 0.5713 (tmm)
  outliers start: 38
  outliers final: 21
  residues processed: 144
  average time/residue: 0.1115
  time to fit residues: 24.9225
Evaluate side-chains
  134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1462 ASN
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.114833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.080310 restraints weight = 31151.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.78
r_work: 0.3106 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15379  Z= 0.120
  Angle     :  0.548  10.078  21312  Z= 0.277
  Chirality :  0.038   0.232   2477
  Planarity :  0.003   0.043   2337
  Dihedral  : 16.985 163.181   3358
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.71 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.21), residues: 1549
  helix:  0.94 (0.19), residues: 751
  sheet: -0.53 (0.36), residues: 186
  loop : -0.76 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 671 
 TYR   0.015   0.001   TYR A1232 
 PHE   0.016   0.001   PHE A1473 
 TRP   0.012   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (15379)
  covalent geometry    : angle       0.54833 (21312)
  hydrogen bonds       : bond        0.03728 (  702)
  hydrogen bonds       : angle       4.36096 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 VAL cc_start: 0.8649 (m) cc_final: 0.8438 (m)
REVERT: A  551 PHE cc_start: 0.8327 (m-80) cc_final: 0.8079 (m-80)
REVERT: A  675 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7459 (tp)
REVERT: A  900 ARG cc_start: 0.7395 (mtt90) cc_final: 0.6416 (mpt90)
REVERT: A  934 HIS cc_start: 0.7442 (t-90) cc_final: 0.6895 (t-90)
REVERT: A  939 MET cc_start: 0.5265 (tpp) cc_final: 0.4956 (tpp)
REVERT: A 1035 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6806 (mm)
REVERT: A 1037 TYR cc_start: 0.6625 (t80) cc_final: 0.6238 (t80)
REVERT: A 1417 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6813 (mpp)
REVERT: A 1435 TYR cc_start: 0.7822 (m-80) cc_final: 0.7608 (m-10)
REVERT: A 1489 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8221 (tt0)
REVERT: A 1604 THR cc_start: 0.4649 (OUTLIER) cc_final: 0.4375 (m)
REVERT: A 1674 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.5596 (mm)
REVERT: A 1681 MET cc_start: 0.6041 (ppp) cc_final: 0.5584 (ppp)
REVERT: A 1682 VAL cc_start: 0.8574 (t) cc_final: 0.8338 (t)
  outliers start: 36
  outliers final: 21
  residues processed: 146
  average time/residue: 0.1156
  time to fit residues: 25.6111
Evaluate side-chains
  140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1462 ASN
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 164 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 144 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 151 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN
A1704 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.112683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.077181 restraints weight = 31589.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.86
r_work: 0.3048 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  15379  Z= 0.201
  Angle     :  0.617   9.457  21312  Z= 0.315
  Chirality :  0.041   0.250   2477
  Planarity :  0.004   0.044   2337
  Dihedral  : 16.990 158.737   3358
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.86 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.21), residues: 1549
  helix:  0.78 (0.19), residues: 743
  sheet: -0.53 (0.37), residues: 182
  loop : -0.71 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1658 
 TYR   0.022   0.002   TYR A1468 
 PHE   0.021   0.002   PHE A1473 
 TRP   0.012   0.002   TRP A 885 
 HIS   0.004   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (15379)
  covalent geometry    : angle       0.61705 (21312)
  hydrogen bonds       : bond        0.04346 (  702)
  hydrogen bonds       : angle       4.56479 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 114
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A  675 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7612 (tp)
REVERT: A  934 HIS cc_start: 0.7541 (t-90) cc_final: 0.6970 (t-90)
REVERT: A  939 MET cc_start: 0.5193 (tpp) cc_final: 0.4873 (tpp)
REVERT: A 1037 TYR cc_start: 0.6669 (t80) cc_final: 0.6262 (t80)
REVERT: A 1417 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6870 (mpp)
REVERT: A 1604 THR cc_start: 0.4933 (OUTLIER) cc_final: 0.4621 (m)
REVERT: A 1681 MET cc_start: 0.6160 (ppp) cc_final: 0.5660 (ppp)
  outliers start: 38
  outliers final: 24
  residues processed: 143
  average time/residue: 0.1202
  time to fit residues: 26.4685
Evaluate side-chains
  133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1176 ILE
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1284 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 52 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 158 optimal weight:    6.9990
   chunk 104 optimal weight:    0.3980
   chunk 159 optimal weight:    8.9990
   chunk 136 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.115073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.080007 restraints weight = 31501.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.89
r_work: 0.3104 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15379  Z= 0.116
  Angle     :  0.570  11.750  21312  Z= 0.286
  Chirality :  0.038   0.231   2477
  Planarity :  0.004   0.046   2337
  Dihedral  : 17.008 161.205   3358
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.71 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.21), residues: 1549
  helix:  0.89 (0.19), residues: 745
  sheet: -0.55 (0.37), residues: 176
  loop : -0.69 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1031 
 TYR   0.023   0.001   TYR A  11 
 PHE   0.015   0.001   PHE A1473 
 TRP   0.015   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (15379)
  covalent geometry    : angle       0.56963 (21312)
  hydrogen bonds       : bond        0.03736 (  702)
  hydrogen bonds       : angle       4.42063 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 VAL cc_start: 0.8624 (m) cc_final: 0.8407 (m)
REVERT: A  504 LEU cc_start: 0.8499 (tt) cc_final: 0.8201 (mt)
REVERT: A  675 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7728 (mt)
REVERT: A  934 HIS cc_start: 0.7413 (t-90) cc_final: 0.6784 (t-90)
REVERT: A  939 MET cc_start: 0.5236 (tpp) cc_final: 0.4922 (tpp)
REVERT: A 1037 TYR cc_start: 0.6651 (t80) cc_final: 0.6256 (t80)
REVERT: A 1417 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6795 (mpp)
REVERT: A 1435 TYR cc_start: 0.7789 (m-80) cc_final: 0.7573 (m-10)
REVERT: A 1544 GLU cc_start: 0.8587 (tp30) cc_final: 0.7851 (mt-10)
REVERT: A 1604 THR cc_start: 0.4372 (OUTLIER) cc_final: 0.4143 (m)
REVERT: A 1674 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.5837 (pt)
REVERT: A 1681 MET cc_start: 0.6053 (ppp) cc_final: 0.5597 (ppp)
REVERT: A 1682 VAL cc_start: 0.8616 (t) cc_final: 0.8371 (t)
  outliers start: 28
  outliers final: 18
  residues processed: 141
  average time/residue: 0.1268
  time to fit residues: 27.0441
Evaluate side-chains
  137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 153 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN
A1704 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.114280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.080289 restraints weight = 31391.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.95
r_work: 0.3069 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15379  Z= 0.147
  Angle     :  0.585  11.401  21312  Z= 0.294
  Chirality :  0.039   0.238   2477
  Planarity :  0.004   0.045   2337
  Dihedral  : 16.968 160.743   3358
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.64 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.21), residues: 1549
  helix:  0.89 (0.19), residues: 745
  sheet: -0.56 (0.37), residues: 182
  loop : -0.72 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 671 
 TYR   0.024   0.001   TYR A  11 
 PHE   0.018   0.001   PHE A1473 
 TRP   0.012   0.001   TRP A1634 
 HIS   0.004   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15379)
  covalent geometry    : angle       0.58528 (21312)
  hydrogen bonds       : bond        0.03911 (  702)
  hydrogen bonds       : angle       4.45127 ( 1925)

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

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

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3098 Ramachandran restraints generated.
    1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 LEU cc_start: 0.8491 (tt) cc_final: 0.8224 (mt)
REVERT: A  536 VAL cc_start: 0.6673 (p) cc_final: 0.6397 (m)
REVERT: A  675 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7878 (mt)
REVERT: A  934 HIS cc_start: 0.7597 (t-90) cc_final: 0.6960 (t-90)
REVERT: A  939 MET cc_start: 0.5247 (tpp) cc_final: 0.4939 (tpp)
REVERT: A 1037 TYR cc_start: 0.6645 (t80) cc_final: 0.6213 (t80)
REVERT: A 1417 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6857 (mpp)
REVERT: A 1544 GLU cc_start: 0.8574 (tp30) cc_final: 0.7777 (mt-10)
REVERT: A 1604 THR cc_start: 0.4163 (OUTLIER) cc_final: 0.3865 (m)
REVERT: A 1681 MET cc_start: 0.6110 (ppp) cc_final: 0.5664 (ppp)
  outliers start: 26
  outliers final: 21
  residues processed: 127
  average time/residue: 0.1171
  time to fit residues: 22.8935
Evaluate side-chains
  136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  675 ILE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1171 VAL
Chi-restraints excluded: chain A residue 1212 LEU
Chi-restraints excluded: chain A residue 1417 MET
Chi-restraints excluded: chain A residue 1494 MET
Chi-restraints excluded: chain A residue 1604 THR
Chi-restraints excluded: chain A residue 1674 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 126 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 160 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 83 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 115 optimal weight:    0.4980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN
A1704 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.116432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.081983 restraints weight = 31253.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.81
r_work: 0.3137 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  15379  Z= 0.107
  Angle     :  0.561  11.473  21312  Z= 0.282
  Chirality :  0.038   0.226   2477
  Planarity :  0.003   0.047   2337
  Dihedral  : 16.983 164.008   3358
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 20.36 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.21), residues: 1549
  helix:  0.97 (0.19), residues: 743
  sheet: -0.56 (0.36), residues: 176
  loop : -0.67 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 671 
 TYR   0.021   0.001   TYR A  11 
 PHE   0.014   0.001   PHE A1473 
 TRP   0.016   0.001   TRP A1634 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (15379)
  covalent geometry    : angle       0.56125 (21312)
  hydrogen bonds       : bond        0.03599 (  702)
  hydrogen bonds       : angle       4.38373 ( 1925)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3316.47 seconds
wall clock time: 57 minutes 54.85 seconds (3474.85 seconds total)