Starting phenix.real_space_refine
on Fri Feb 14 17:03:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iv6_9742/02_2025/6iv6_9742.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      26      5.49       5
     S      21      5.16       5
     C    6406      2.51       5
     N    1722      2.21       5
     O    1983      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10158
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1209, 9611
          Classifications: {'peptide': 1209}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'CIS': 4, 'PTRANS': 35, 'TRANS': 1169}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 267
          Unresolved non-hydrogen angles: 338
          Unresolved non-hydrogen dihedrals: 229
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'ALY:plan-2': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'HIS:plan': 7}
          Unresolved non-hydrogen planarities: 178
    Chain: "G"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 547
          Classifications: {'RNA': 26}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 8, 'rna3p': 17}
  Time building chain proxies: 6.81, per 1000 atoms: 0.67
  Number of scatterers: 10158
  At special positions: 0
  Unit cell: (110.39, 101.26, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P      26     15.00
     O    1983      8.00
     N    1722      7.00
     C    6406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.56
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      42.0% alpha, 7.9% beta
      6 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 3.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 34
    Processing helix  chain 'A' and resid 34 through 65
      removed outlier: 4.460A  pdb=" N   GLN A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LYS A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
      removed outlier: 3.616A  pdb=" N   LEU A  81 " --> pdb=" O   TYR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 109
      removed outlier: 4.212A  pdb=" N   GLU A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 163 through 168
      removed outlier: 3.864A  pdb=" N   TYR A 166 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE A 167 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 168 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 163 through 168'
    Processing helix  chain 'A' and resid 169 through 175
      removed outlier: 3.949A  pdb=" N   ASN A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 193
      removed outlier: 3.794A  pdb=" N   ARG A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.676A  pdb=" N   ARG A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.838A  pdb=" N   ILE A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN A 222 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.699A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 244
      removed outlier: 3.891A  pdb=" N   LEU A 244 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.654A  pdb=" N   ALA A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.503A  pdb=" N   ASN A 276 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 326
      removed outlier: 3.934A  pdb=" N   VAL A 319 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS A 320 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN A 324 " --> pdb=" O   CYS A 320 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLU A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 343
      removed outlier: 3.664A  pdb=" N   GLY A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 357
      No H-bonds generated for 'chain 'A' and resid 355 through 357'
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 371 through 380
    Processing helix  chain 'A' and resid 381 through 385
      removed outlier: 3.850A  pdb=" N   VAL A 384 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 385 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 381 through 385'
    Processing helix  chain 'A' and resid 425 through 432
      removed outlier: 3.667A  pdb=" N   TYR A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR A 430 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A 432 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 425 through 432'
    Processing helix  chain 'A' and resid 455 through 460
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 501 through 511
      removed outlier: 3.656A  pdb=" N   LEU A 505 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN A 506 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 539
      removed outlier: 4.002A  pdb=" N   GLU A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ALA A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP A 536 " --> pdb=" O   GLY A 532 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 553
      removed outlier: 3.689A  pdb=" N   LEU A 544 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 584
      removed outlier: 3.981A  pdb=" N   ASN A 583 " --> pdb=" O   LYS A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 633
      removed outlier: 3.645A  pdb=" N   LEU A 633 " --> pdb=" O   PRO A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 657
    Processing helix  chain 'A' and resid 659 through 663
      removed outlier: 3.603A  pdb=" N   LYS A 662 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS A 663 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 659 through 663'
    Processing helix  chain 'A' and resid 669 through 686
      removed outlier: 3.848A  pdb=" N   ILE A 676 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASP A 677 " --> pdb=" O   HIS A 673 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 678 " --> pdb=" O   ALA A 674 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN A 684 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   HIS A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 716
      removed outlier: 3.554A  pdb=" N   VAL A 712 " --> pdb=" O   PHE A 708 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 713 " --> pdb=" O   TYR A 709 " (cutoff:3.500A)
      Proline residue:  A 714  - end of helix
    Processing helix  chain 'A' and resid 725 through 734
      removed outlier: 3.534A  pdb=" N   ILE A 729 " --> pdb=" O   ASN A 725 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU A 734 " --> pdb=" O   ASN A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 749
      removed outlier: 3.731A  pdb=" N   SER A 749 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 764
      removed outlier: 3.519A  pdb=" N   TYR A 762 " --> pdb=" O   LEU A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 772
      removed outlier: 3.514A  pdb=" N   LEU A 772 " --> pdb=" O   GLU A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 831
      removed outlier: 4.124A  pdb=" N   GLN A 831 " --> pdb=" O   LYS A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 854
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 915 through 926
      removed outlier: 3.538A  pdb=" N   ILE A 924 " --> pdb=" O   ASP A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 962
      removed outlier: 3.855A  pdb=" N   THR A 938 " --> pdb=" O   GLY A 934 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 939 " --> pdb=" O   GLU A 935 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS A 940 " --> pdb=" O   ILE A 936 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER A 948 " --> pdb=" O   SER A 944 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   HIS A 949 " --> pdb=" O   GLY A 945 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   HIS A 952 " --> pdb=" O   SER A 948 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A 959 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS A 960 " --> pdb=" O   GLN A 956 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 961 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 999
      removed outlier: 4.006A  pdb=" N   ASN A 988 " --> pdb=" O   GLN A 984 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE A 994 " --> pdb=" O   GLU A 990 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   HIS A 999 " --> pdb=" O   LYS A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1072
      removed outlier: 3.778A  pdb=" N   GLN A1068 " --> pdb=" O   ILE A1064 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ALA A1069 " --> pdb=" O   ALA A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1138
    Processing helix  chain 'A' and resid 1154 through 1159
      removed outlier: 3.602A  pdb=" N   ILE A1158 " --> pdb=" O   LEU A1154 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   CYS A1159 " --> pdb=" O   VAL A1155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1154 through 1159'
    Processing helix  chain 'A' and resid 1165 through 1179
      removed outlier: 3.667A  pdb=" N   LEU A1177 " --> pdb=" O   LEU A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1216 through 1238
      removed outlier: 3.579A  pdb=" N   GLY A1221 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A1222 " --> pdb=" O   ASP A1218 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE A1225 " --> pdb=" O   GLY A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1260
      removed outlier: 3.552A  pdb=" N   LEU A1255 " --> pdb=" O   ASN A1251 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN A1259 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASN A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 721 through 724
      removed outlier: 3.527A  pdb=" N   MET A 621 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ILE A 587 " --> pdb=" O   MET A 621 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   TYR A 594 " --> pdb=" O   ILE A 743 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564
      removed outlier: 4.624A  pdb=" N   ILE A 785 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 625
    Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 897
      removed outlier: 6.879A  pdb=" N   VAL A 885 " --> pdb=" O   LEU A 893 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLN A 895 " --> pdb=" O   LEU A 883 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU A 883 " --> pdb=" O   GLN A 895 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   SER A 897 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   LEU A 881 " --> pdb=" O   SER A 897 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLU A 968 " --> pdb=" O   ILE A 873 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   ARG A 875 " --> pdb=" O   GLU A 968 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 900 through 905
      removed outlier: 3.755A  pdb=" N   ILE A 901 " --> pdb=" O   THR A 913 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 913 " --> pdb=" O   ILE A 901 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   THR A 903 " --> pdb=" O   MET A 911 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   MET A 911 " --> pdb=" O   THR A 903 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1077 through 1079
      removed outlier: 3.818A  pdb=" N   ILE A1090 " --> pdb=" O   TRP A1106 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TRP A1106 " --> pdb=" O   ILE A1090 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1181 through 1183

    294 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 3.68

  Time building geometry restraints manager: 2.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2749
        1.33 -     1.45: 2062
        1.45 -     1.57: 5529
        1.57 -     1.69: 52
        1.69 -     1.81: 35
  Bond restraints: 10427
  Sorted by residual:
  bond pdb=" C   ALY A 153 "
       pdb=" O   ALY A 153 "
    ideal  model  delta    sigma   weight residual
    1.231  1.363 -0.132 2.00e-02 2.50e+03 4.35e+01
  bond pdb=" C   ALY A 635 "
       pdb=" O   ALY A 635 "
    ideal  model  delta    sigma   weight residual
    1.231  1.360 -0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C   ALY A 816 "
       pdb=" O   ALY A 816 "
    ideal  model  delta    sigma   weight residual
    1.231  1.359 -0.128 2.00e-02 2.50e+03 4.09e+01
  bond pdb=" N   GLN A 281 "
       pdb=" CA  GLN A 281 "
    ideal  model  delta    sigma   weight residual
    1.459  1.505 -0.046 1.20e-02 6.94e+03 1.44e+01
  bond pdb=" N   ASN A 280 "
       pdb=" CA  ASN A 280 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.20e-02 6.94e+03 9.44e+00
  ... (remaining 10422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 13919
        3.08 -     6.17: 241
        6.17 -     9.25: 32
        9.25 -    12.33: 9
       12.33 -    15.41: 3
  Bond angle restraints: 14204
  Sorted by residual:
  angle pdb=" C   THR A 518 "
        pdb=" N   THR A 519 "
        pdb=" CA  THR A 519 "
      ideal   model   delta    sigma   weight residual
     121.70  136.98  -15.28 1.80e+00 3.09e-01 7.21e+01
  angle pdb=" O   ALY A 635 "
        pdb=" C   ALY A 635 "
        pdb=" N   VAL A 636 "
      ideal   model   delta    sigma   weight residual
     123.00  111.47   11.53 1.60e+00 3.91e-01 5.19e+01
  angle pdb=" CA  ALY A 153 "
        pdb=" C   ALY A 153 "
        pdb=" O   ALY A 153 "
      ideal   model   delta    sigma   weight residual
     120.80  109.97   10.83 1.70e+00 3.46e-01 4.06e+01
  angle pdb=" C   GLY A 120 "
        pdb=" N   TYR A 121 "
        pdb=" CA  TYR A 121 "
      ideal   model   delta    sigma   weight residual
     121.54  132.60  -11.06 1.91e+00 2.74e-01 3.35e+01
  angle pdb=" C   GLN A 281 "
        pdb=" N   HIS A 282 "
        pdb=" CA  HIS A 282 "
      ideal   model   delta    sigma   weight residual
     121.70  131.91  -10.21 1.80e+00 3.09e-01 3.22e+01
  ... (remaining 14199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 6061
       35.87 -    71.73: 183
       71.73 -   107.60: 17
      107.60 -   143.47: 1
      143.47 -   179.33: 3
  Dihedral angle restraints: 6265
    sinusoidal: 2725
      harmonic: 3540
  Sorted by residual:
  dihedral pdb=" O4'   C G  23 "
           pdb=" C1'   C G  23 "
           pdb=" N1    C G  23 "
           pdb=" C2    C G  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   51.91  148.09     1      1.50e+01 4.44e-03 7.89e+01
  dihedral pdb=" O4'   U G  16 "
           pdb=" C1'   U G  16 "
           pdb=" N1    U G  16 "
           pdb=" C2    U G  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.67  179.33     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U G  15 "
           pdb=" C1'   U G  15 "
           pdb=" N1    U G  15 "
           pdb=" C2    U G  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.81 -176.81     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1338
       0.074 -    0.148: 199
       0.148 -    0.223: 21
       0.223 -    0.297: 5
       0.297 -    0.371: 1
  Chirality restraints: 1564
  Sorted by residual:
  chirality pdb=" CB  ILE A1029 "
            pdb=" CA  ILE A1029 "
            pdb=" CG1 ILE A1029 "
            pdb=" CG2 ILE A1029 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.44e+00
  chirality pdb=" CA  ASP A 665 "
            pdb=" N   ASP A 665 "
            pdb=" C   ASP A 665 "
            pdb=" CB  ASP A 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CB  THR A 516 "
            pdb=" CA  THR A 516 "
            pdb=" OG1 THR A 516 "
            pdb=" CG2 THR A 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1561 not shown)

  Planarity restraints: 1754
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALY A 153 "    0.080 2.00e-02 2.50e+03   1.55e-01 2.41e+02
        pdb=" C   ALY A 153 "   -0.269 2.00e-02 2.50e+03
        pdb=" O   ALY A 153 "    0.090 2.00e-02 2.50e+03
        pdb=" N   LEU A 154 "    0.099 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALY A 635 "    0.083 2.00e-02 2.50e+03   1.53e-01 2.35e+02
        pdb=" C   ALY A 635 "   -0.265 2.00e-02 2.50e+03
        pdb=" O   ALY A 635 "    0.089 2.00e-02 2.50e+03
        pdb=" N   VAL A 636 "    0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 112 "   -0.023 2.00e-02 2.50e+03   4.75e-02 2.25e+01
        pdb=" C   GLY A 112 "    0.082 2.00e-02 2.50e+03
        pdb=" O   GLY A 112 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ASN A 113 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1751 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2513
        2.79 -     3.32: 8624
        3.32 -     3.84: 15950
        3.84 -     4.37: 18856
        4.37 -     4.90: 31975
  Nonbonded interactions: 77918
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 623 "
            pdb=" O   LEU A 779 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR A  10 "
            pdb=" OD1 ASN A 998 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   THR A 208 "
            pdb=" OG  SER A 214 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   LYS A 512 "
            pdb=" OG1 THR A 515 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OH  TYR A 353 "
            pdb=" OD1 ASN A 522 "
     model   vdw
     2.342 3.040
  ... (remaining 77913 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.920
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.132  10427  Z= 0.360
  Angle     :  1.041  15.413  14204  Z= 0.578
  Chirality :  0.053   0.371   1564
  Planarity :  0.008   0.155   1754
  Dihedral  : 17.648 179.332   3987
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.66 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.38 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.17 (0.17), residues: 1187
  helix: -4.23 (0.11), residues: 426
  sheet: -2.75 (0.43), residues: 124
  loop : -3.01 (0.19), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1042 
 HIS   0.006   0.001   HIS A 193 
 PHE   0.020   0.002   PHE A  18 
 TYR   0.034   0.002   TYR A 327 
 ARG   0.007   0.001   ARG A 328 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7129 (t0) cc_final: 0.6854 (t0)
REVERT: A  162 LYS cc_start: 0.6627 (mttt) cc_final: 0.5393 (mmtt)
REVERT: A  293 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6771 (mtm180)
REVERT: A  380 TYR cc_start: 0.4658 (m-80) cc_final: 0.2956 (t80)
REVERT: A  498 LYS cc_start: 0.7230 (pptt) cc_final: 0.5649 (mmmm)
REVERT: A  560 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6464 (mt-10)
REVERT: A  894 GLU cc_start: 0.8383 (pt0) cc_final: 0.8165 (tt0)
REVERT: A  921 LYS cc_start: 0.5492 (ttpt) cc_final: 0.5243 (mtmt)
REVERT: A 1061 TYR cc_start: 0.7244 (t80) cc_final: 0.6786 (t80)
REVERT: A 1104 GLN cc_start: 0.7497 (mt0) cc_final: 0.7268 (mt0)
REVERT: A 1113 ASP cc_start: 0.7285 (t70) cc_final: 0.6663 (t70)
REVERT: A 1115 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7252 (mmt90)
REVERT: A 1243 ASN cc_start: 0.5276 (t0) cc_final: 0.5013 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 171
  average time/residue: 0.2633
  time to fit residues: 61.6089
Evaluate side-chains
  117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue 1216 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 159 HIS
A 204 GLN
A 219 GLN
A 236 HIS
A 269 GLN
A 279 HIS
A 296 HIS
A 506 ASN
A 526 ASN
A 612 ASN
A 619 GLN
A 642 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A 742 GLN
A 843 ASN
A 859 ASN
A 910 GLN
A1018 GLN
A1043 ASN
A1089 HIS

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.181745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.177574 restraints weight = 12591.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.175928 restraints weight = 20664.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.167122 restraints weight = 26099.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  10427  Z= 0.381
  Angle     :  0.776  12.028  14204  Z= 0.396
  Chirality :  0.047   0.202   1564
  Planarity :  0.005   0.048   1754
  Dihedral  : 15.238 174.213   1714
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.85 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.14 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.19), residues: 1187
  helix: -2.61 (0.18), residues: 424
  sheet: -2.62 (0.46), residues: 117
  loop : -2.73 (0.20), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1106 
 HIS   0.012   0.002   HIS A 509 
 PHE   0.021   0.002   PHE A  18 
 TYR   0.023   0.002   TYR A 327 
 ARG   0.008   0.001   ARG A 104 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8060 (ttm) cc_final: 0.7824 (ttt)
REVERT: A  162 LYS cc_start: 0.6997 (mttt) cc_final: 0.5971 (mmtt)
REVERT: A  328 ARG cc_start: 0.5256 (mmm160) cc_final: 0.4938 (mtp180)
REVERT: A  380 TYR cc_start: 0.4908 (m-80) cc_final: 0.3787 (t80)
REVERT: A  460 LYS cc_start: 0.5330 (mmtp) cc_final: 0.4931 (mmtp)
REVERT: A  498 LYS cc_start: 0.7993 (pptt) cc_final: 0.6934 (tptm)
REVERT: A  794 MET cc_start: 0.7663 (mmm) cc_final: 0.7438 (mmm)
REVERT: A  894 GLU cc_start: 0.8727 (pt0) cc_final: 0.8455 (pt0)
REVERT: A  921 LYS cc_start: 0.6491 (ttpt) cc_final: 0.6101 (mttt)
REVERT: A  935 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6423 (mp0)
REVERT: A 1083 ARG cc_start: 0.6072 (mmm160) cc_final: 0.5838 (mtp85)
REVERT: A 1115 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7768 (mmt90)
REVERT: A 1208 LEU cc_start: 0.7105 (tt) cc_final: 0.6802 (tp)
  outliers start: 34
  outliers final: 17
  residues processed: 136
  average time/residue: 0.2349
  time to fit residues: 45.1346
Evaluate side-chains
  114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0020
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
A 269 GLN
A 276 ASN
A 459 GLN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 HIS
A 869 ASN
A1198 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.191814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.187470 restraints weight = 12538.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.180331 restraints weight = 20224.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.177736 restraints weight = 18979.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10427  Z= 0.152
  Angle     :  0.590  10.125  14204  Z= 0.298
  Chirality :  0.041   0.194   1564
  Planarity :  0.003   0.037   1754
  Dihedral  : 14.860 178.583   1712
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.26 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.22), residues: 1187
  helix: -1.28 (0.23), residues: 430
  sheet: -2.57 (0.46), residues: 125
  loop : -2.50 (0.21), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 575 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.013   0.001   PHE A  18 
 TYR   0.025   0.001   TYR A 121 
 ARG   0.004   0.000   ARG A 104 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5993 (tmm)
REVERT: A   42 MET cc_start: 0.7858 (ttm) cc_final: 0.7590 (ttt)
REVERT: A  162 LYS cc_start: 0.6881 (mttt) cc_final: 0.5969 (mmtt)
REVERT: A  328 ARG cc_start: 0.4904 (mmm160) cc_final: 0.4654 (mtp180)
REVERT: A  362 LEU cc_start: 0.7729 (tt) cc_final: 0.7467 (tp)
REVERT: A  380 TYR cc_start: 0.4751 (m-80) cc_final: 0.3615 (t80)
REVERT: A  460 LYS cc_start: 0.5170 (mmtp) cc_final: 0.4830 (mmtp)
REVERT: A  498 LYS cc_start: 0.7822 (pptt) cc_final: 0.6811 (tptm)
REVERT: A  921 LYS cc_start: 0.6271 (ttpt) cc_final: 0.6003 (mttt)
REVERT: A 1115 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7606 (mmt90)
REVERT: A 1208 LEU cc_start: 0.7128 (tt) cc_final: 0.6839 (tp)
  outliers start: 32
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2436
  time to fit residues: 48.2018
Evaluate side-chains
  111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 112 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 GLN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 ASN
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.183032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.178738 restraints weight = 12489.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.178053 restraints weight = 23561.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.169154 restraints weight = 22109.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10427  Z= 0.331
  Angle     :  0.707  11.251  14204  Z= 0.358
  Chirality :  0.046   0.193   1564
  Planarity :  0.005   0.079   1754
  Dihedral  : 15.056 172.819   1712
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 18.26 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.22), residues: 1187
  helix: -1.26 (0.23), residues: 449
  sheet: -2.58 (0.47), residues: 123
  loop : -2.56 (0.22), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 575 
 HIS   0.005   0.001   HIS A 759 
 PHE   0.031   0.002   PHE A 344 
 TYR   0.021   0.002   TYR A 356 
 ARG   0.004   0.000   ARG A  17 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8053 (ttm) cc_final: 0.7810 (ttt)
REVERT: A  162 LYS cc_start: 0.6928 (mttt) cc_final: 0.6060 (mmtt)
REVERT: A  328 ARG cc_start: 0.5270 (mmm160) cc_final: 0.4942 (mtp180)
REVERT: A  498 LYS cc_start: 0.7861 (pptt) cc_final: 0.6902 (mmtp)
REVERT: A 1208 LEU cc_start: 0.7381 (tt) cc_final: 0.7110 (tp)
  outliers start: 49
  outliers final: 33
  residues processed: 141
  average time/residue: 0.2296
  time to fit residues: 46.2839
Evaluate side-chains
  130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  269 GLN
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  784 GLU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.186577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.182570 restraints weight = 12431.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.181630 restraints weight = 19579.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.180791 restraints weight = 23344.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10427  Z= 0.193
  Angle     :  0.611  11.056  14204  Z= 0.307
  Chirality :  0.042   0.190   1564
  Planarity :  0.004   0.055   1754
  Dihedral  : 14.913 175.554   1712
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 20.08 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.23), residues: 1187
  helix: -0.83 (0.24), residues: 449
  sheet: -2.42 (0.47), residues: 123
  loop : -2.45 (0.22), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 933 
 HIS   0.005   0.001   HIS A 156 
 PHE   0.023   0.001   PHE A 344 
 TYR   0.016   0.001   TYR A 121 
 ARG   0.005   0.000   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8048 (ttm) cc_final: 0.7746 (ttt)
REVERT: A  162 LYS cc_start: 0.6978 (mttt) cc_final: 0.6154 (mmtt)
REVERT: A  328 ARG cc_start: 0.4783 (mmm160) cc_final: 0.4396 (mtp-110)
REVERT: A  380 TYR cc_start: 0.5022 (m-80) cc_final: 0.3714 (t80)
REVERT: A  495 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5961 (tmm160)
REVERT: A  498 LYS cc_start: 0.7742 (pptt) cc_final: 0.6795 (mmtp)
REVERT: A 1208 LEU cc_start: 0.7319 (tt) cc_final: 0.7074 (tp)
  outliers start: 37
  outliers final: 27
  residues processed: 132
  average time/residue: 0.2654
  time to fit residues: 50.6950
Evaluate side-chains
  122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.181367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.179778 restraints weight = 12720.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.163748 restraints weight = 27779.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.162973 restraints weight = 35506.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10427  Z= 0.354
  Angle     :  0.718  11.712  14204  Z= 0.361
  Chirality :  0.047   0.192   1564
  Planarity :  0.004   0.060   1754
  Dihedral  : 15.103 172.430   1712
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 19.48 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.23), residues: 1187
  helix: -0.99 (0.24), residues: 440
  sheet: -2.47 (0.48), residues: 122
  loop : -2.41 (0.22), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 933 
 HIS   0.009   0.001   HIS A 509 
 PHE   0.024   0.002   PHE A 344 
 TYR   0.022   0.002   TYR A1116 
 ARG   0.007   0.001   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 97
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8076 (ttm) cc_final: 0.7793 (ttt)
REVERT: A  328 ARG cc_start: 0.5211 (mmm160) cc_final: 0.4655 (mtp-110)
REVERT: A  495 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6153 (tmm160)
REVERT: A 1208 LEU cc_start: 0.7426 (tt) cc_final: 0.7184 (tp)
  outliers start: 57
  outliers final: 43
  residues processed: 145
  average time/residue: 0.2330
  time to fit residues: 48.3402
Evaluate side-chains
  136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 92
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  269 GLN
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 105 optimal weight:    0.4980
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 949 HIS
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.185021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.180038 restraints weight = 12552.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.178806 restraints weight = 23310.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.178006 restraints weight = 23835.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10427  Z= 0.246
  Angle     :  0.649  11.277  14204  Z= 0.325
  Chirality :  0.044   0.200   1564
  Planarity :  0.004   0.054   1754
  Dihedral  : 14.980 173.804   1712
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.38 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.23), residues: 1187
  helix: -0.77 (0.24), residues: 440
  sheet: -2.38 (0.48), residues: 122
  loop : -2.37 (0.22), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 575 
 HIS   0.007   0.001   HIS A 509 
 PHE   0.022   0.001   PHE A 344 
 TYR   0.016   0.002   TYR A1116 
 ARG   0.007   0.000   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 95
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8033 (ttm) cc_final: 0.7756 (ttt)
REVERT: A  162 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7568 (mtmm)
REVERT: A  495 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6073 (tmm160)
REVERT: A  498 LYS cc_start: 0.7535 (pptt) cc_final: 0.6609 (tppp)
REVERT: A 1208 LEU cc_start: 0.7282 (tt) cc_final: 0.7054 (tp)
  outliers start: 54
  outliers final: 42
  residues processed: 141
  average time/residue: 0.2319
  time to fit residues: 47.7068
Evaluate side-chains
  133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 89
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  162 LYS
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1043 ASN
A1251 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.185350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.181427 restraints weight = 12594.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.180671 restraints weight = 18532.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.179633 restraints weight = 20902.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10427  Z= 0.202
  Angle     :  0.612  10.978  14204  Z= 0.306
  Chirality :  0.042   0.188   1564
  Planarity :  0.003   0.037   1754
  Dihedral  : 14.821 175.775   1712
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.18 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.23), residues: 1187
  helix: -0.56 (0.25), residues: 438
  sheet: -2.25 (0.49), residues: 122
  loop : -2.33 (0.23), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 575 
 HIS   0.005   0.001   HIS A 509 
 PHE   0.020   0.001   PHE A 344 
 TYR   0.014   0.001   TYR A 121 
 ARG   0.006   0.000   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 100
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7802 (m-80)
REVERT: A 1208 LEU cc_start: 0.7311 (tt) cc_final: 0.7066 (tp)
  outliers start: 54
  outliers final: 43
  residues processed: 146
  average time/residue: 0.2011
  time to fit residues: 43.8118
Evaluate side-chains
  134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 90
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 113 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 114 optimal weight:    0.4980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.186705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.182822 restraints weight = 12611.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.170297 restraints weight = 20400.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.167392 restraints weight = 21919.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10427  Z= 0.180
  Angle     :  0.604  10.985  14204  Z= 0.301
  Chirality :  0.041   0.187   1564
  Planarity :  0.003   0.034   1754
  Dihedral  : 14.677 176.574   1712
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.99 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.24), residues: 1187
  helix: -0.36 (0.25), residues: 438
  sheet: -2.14 (0.49), residues: 122
  loop : -2.23 (0.23), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 575 
 HIS   0.010   0.001   HIS A 509 
 PHE   0.019   0.001   PHE A 344 
 TYR   0.014   0.001   TYR A 121 
 ARG   0.006   0.000   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 ASN cc_start: 0.4500 (t0) cc_final: 0.4192 (t0)
REVERT: A  166 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7850 (m-80)
REVERT: A  372 LEU cc_start: 0.7785 (tt) cc_final: 0.7545 (tt)
REVERT: A 1208 LEU cc_start: 0.7299 (tt) cc_final: 0.7050 (tp)
  outliers start: 47
  outliers final: 38
  residues processed: 135
  average time/residue: 0.1919
  time to fit residues: 38.7510
Evaluate side-chains
  132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 962 ASN
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.180642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.179095 restraints weight = 12647.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.162217 restraints weight = 24361.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.161133 restraints weight = 27479.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10427  Z= 0.363
  Angle     :  0.741  14.600  14204  Z= 0.370
  Chirality :  0.047   0.282   1564
  Planarity :  0.004   0.047   1754
  Dihedral  : 14.882 171.650   1712
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.87 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 21.49 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.23), residues: 1187
  helix: -0.73 (0.25), residues: 437
  sheet: -2.19 (0.48), residues: 124
  loop : -2.36 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A1042 
 HIS   0.011   0.002   HIS A 509 
 PHE   0.022   0.002   PHE A 972 
 TYR   0.020   0.002   TYR A1116 
 ARG   0.007   0.001   ARG A 474 

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 92
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 ASN cc_start: 0.4337 (t0) cc_final: 0.4030 (t0)
REVERT: A  166 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7859 (m-80)
REVERT: A 1208 LEU cc_start: 0.7546 (tt) cc_final: 0.7303 (tp)
  outliers start: 48
  outliers final: 43
  residues processed: 134
  average time/residue: 0.2141
  time to fit residues: 41.5570
Evaluate side-chains
  131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 87
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  269 GLN
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 68 optimal weight:    0.0470
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 114 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.188558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.184686 restraints weight = 12387.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.172199 restraints weight = 21164.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.170083 restraints weight = 25299.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10427  Z= 0.171
  Angle     :  0.622  12.517  14204  Z= 0.311
  Chirality :  0.042   0.254   1564
  Planarity :  0.003   0.035   1754
  Dihedral  : 14.706 175.232   1712
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.70 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.24), residues: 1187
  helix: -0.46 (0.25), residues: 443
  sheet: -2.14 (0.49), residues: 122
  loop : -2.27 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A1042 
 HIS   0.010   0.001   HIS A 509 
 PHE   0.019   0.001   PHE A 344 
 TYR   0.028   0.001   TYR A 121 
 ARG   0.006   0.000   ARG A 474 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2814.86 seconds
wall clock time: 51 minutes 28.00 seconds (3088.00 seconds total)