Starting phenix.real_space_refine
on Thu Jul 31 12:40:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r6u_18963/07_2025/8r6u_18963.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      41      5.49       5
     Mg      1      5.21       5
     S      72      5.16       5
     C    8346      2.51       5
     N    2338      2.21       5
     O    2610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13408
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12495
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1566, 12479
          Classifications: {'peptide': 1566}
          Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 1566, 12479
          Classifications: {'peptide': 1566}
          Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 12726
    Chain: "P"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 341
          Classifications: {'RNA': 16}
          Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 6, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 3, 'rna3p': 12}
    Chain: "T"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 361
          Classifications: {'RNA': 17}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 6, 'rna3p': 10}
    Chain: "G"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 81
          Classifications: {'RNA': 4}
          Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 3}
    Chain: "E"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 129
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.68, per 1000 atoms: 1.02
  Number of scatterers: 13408
  At special positions: 0
  Unit cell: (101.15, 109.65, 127.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      72     16.00
     P      41     15.00
     Mg      1     11.99
     O    2610      8.00
     N    2338      7.00
     C    8346      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: 3.90
  Conformation dependent library (CDL) restraints added in 3.5 seconds
  

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2948

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 14 sheets defined
      55.1% alpha, 11.0% beta
      10 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 5.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 5.138A  pdb=" N   TYR A  76 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 85
      removed outlier: 3.851A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 149
      removed outlier: 3.945A  pdb=" N   LEU A 138 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 157
      removed outlier: 3.728A  pdb=" N   ARG A 156 " --> pdb=" O   PRO A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 209
      removed outlier: 3.512A  pdb=" N   MET A 208 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 237 through 245
    Processing helix  chain 'A' and resid 249 through 259
      removed outlier: 4.196A  pdb=" N   LEU A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 285
    Processing helix  chain 'A' and resid 292 through 317
      removed outlier: 3.774A  pdb=" N   ILE A 299 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   CYS A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 359 through 375
    Processing helix  chain 'A' and resid 383 through 393
      removed outlier: 3.808A  pdb=" N   GLU A 387 " --> pdb=" O   ASP A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 436 through 446
      removed outlier: 3.710A  pdb=" N   GLN A 440 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 466
      removed outlier: 3.853A  pdb=" N   THR A 464 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 491
    Processing helix  chain 'A' and resid 496 through 510
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 3.984A  pdb=" N   TRP A 520 " --> pdb=" O   GLN A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 575
      No H-bonds generated for 'chain 'A' and resid 573 through 575'
    Processing helix  chain 'A' and resid 606 through 611
    Processing helix  chain 'A' and resid 611 through 627
    Processing helix  chain 'A' and resid 639 through 655
    Processing helix  chain 'A' and resid 656 through 665
    Processing helix  chain 'A' and resid 665 through 671
      removed outlier: 3.562A  pdb=" N   THR A 669 " --> pdb=" O   LEU A 665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 675
      removed outlier: 3.535A  pdb=" N   VAL A 675 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 672 through 675'
    Processing helix  chain 'A' and resid 682 through 689
      removed outlier: 3.783A  pdb=" N   LYS A 685 " --> pdb=" O   LYS A 682 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET A 686 " --> pdb=" O   PRO A 683 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A 687 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY A 688 " --> pdb=" O   LYS A 685 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS A 689 " --> pdb=" O   MET A 686 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 682 through 689'
    Processing helix  chain 'A' and resid 696 through 716
    Processing helix  chain 'A' and resid 742 through 749
    Processing helix  chain 'A' and resid 750 through 756
      removed outlier: 4.821A  pdb=" N   GLY A 753 " --> pdb=" O   TRP A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 766
    Processing helix  chain 'A' and resid 767 through 776
    Processing helix  chain 'A' and resid 777 through 781
    Processing helix  chain 'A' and resid 802 through 822
    Processing helix  chain 'A' and resid 824 through 839
      removed outlier: 3.573A  pdb=" N   ASN A 828 " --> pdb=" O   GLN A 824 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLU A 831 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 846
      removed outlier: 3.825A  pdb=" N   LEU A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 865
    Processing helix  chain 'A' and resid 874 through 885
    Processing helix  chain 'A' and resid 889 through 903
      removed outlier: 4.041A  pdb=" N   GLY A 894 " --> pdb=" O   ILE A 890 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   GLN A 895 " --> pdb=" O   ASP A 891 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS A 898 " --> pdb=" O   GLY A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 945
      removed outlier: 4.151A  pdb=" N   GLY A 935 " --> pdb=" O   LEU A 931 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL A 936 " --> pdb=" O   VAL A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 974
      removed outlier: 5.601A  pdb=" N   ILE A 962 " --> pdb=" O   LYS A 958 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 963 " --> pdb=" O   ASN A 959 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY A 966 " --> pdb=" O   ILE A 962 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU A 967 " --> pdb=" O   GLU A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 993
      removed outlier: 3.944A  pdb=" N   HIS A 993 " --> pdb=" O   TRP A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1005
      removed outlier: 4.088A  pdb=" N   LEU A 998 " --> pdb=" O   TYR A 994 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE A1005 " --> pdb=" O   VAL A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1020
      removed outlier: 3.888A  pdb=" N   MET A1020 " --> pdb=" O   ALA A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1023
      No H-bonds generated for 'chain 'A' and resid 1021 through 1023'
    Processing helix  chain 'A' and resid 1029 through 1039
      removed outlier: 3.635A  pdb=" N   LYS A1039 " --> pdb=" O   HIS A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1058
      removed outlier: 3.946A  pdb=" N   GLU A1050 " --> pdb=" O   ASP A1046 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1108
    Processing helix  chain 'A' and resid 1109 through 1113
      removed outlier: 3.521A  pdb=" N   GLY A1112 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1155
      removed outlier: 3.999A  pdb=" N   VAL A1143 " --> pdb=" O   ASP A1139 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ARG A1144 " --> pdb=" O   MET A1140 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A1155 " --> pdb=" O   ASN A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1160
    Processing helix  chain 'A' and resid 1161 through 1164
    Processing helix  chain 'A' and resid 1194 through 1200
      removed outlier: 4.311A  pdb=" N   TRP A1198 " --> pdb=" O   PRO A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1212
      No H-bonds generated for 'chain 'A' and resid 1210 through 1212'
    Processing helix  chain 'A' and resid 1213 through 1228
      removed outlier: 3.855A  pdb=" N   ASP A1217 " --> pdb=" O   SER A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1250
    Processing helix  chain 'A' and resid 1257 through 1266
    Processing helix  chain 'A' and resid 1280 through 1284
      removed outlier: 3.602A  pdb=" N   ALA A1284 " --> pdb=" O   PRO A1281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1288 through 1297
    Processing helix  chain 'A' and resid 1302 through 1315
      removed outlier: 3.521A  pdb=" N   ILE A1313 " --> pdb=" O   TYR A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1345 through 1356
      removed outlier: 3.746A  pdb=" N   MET A1355 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A1356 " --> pdb=" O   LEU A1352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1360 through 1368
    Processing helix  chain 'A' and resid 1369 through 1373
    Processing helix  chain 'A' and resid 1378 through 1390
    Processing helix  chain 'A' and resid 1392 through 1397
      removed outlier: 3.854A  pdb=" N   SER A1397 " --> pdb=" O   PRO A1393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1411
      removed outlier: 3.581A  pdb=" N   ARG A1407 " --> pdb=" O   HIS A1403 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A1411 " --> pdb=" O   ARG A1407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1437 through 1448
    Processing helix  chain 'A' and resid 1449 through 1451
      No H-bonds generated for 'chain 'A' and resid 1449 through 1451'
    Processing helix  chain 'A' and resid 1457 through 1465
      removed outlier: 3.955A  pdb=" N   MET A1463 " --> pdb=" O   ASN A1459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1469 through 1478
    Processing helix  chain 'A' and resid 1512 through 1522
    Processing helix  chain 'A' and resid 1534 through 1546
      removed outlier: 3.587A  pdb=" N   ALA A1543 " --> pdb=" O   ASP A1539 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   SER A1544 " --> pdb=" O   LYS A1540 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   PHE A1545 " --> pdb=" O   LEU A1541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1551 through 1559
      removed outlier: 3.625A  pdb=" N   ASP A1558 " --> pdb=" O   GLU A1554 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLY A1559 " --> pdb=" O   THR A1555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1563 through 1575
      removed outlier: 3.871A  pdb=" N   ASN A1569 " --> pdb=" O   VAL A1565 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASP A1575 " --> pdb=" O   ILE A1571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1595 through 1604
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24
      removed outlier: 6.748A  pdb=" N   ILE A 122 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   GLY A 168 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL A 124 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   GLU A 126 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER A 128 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL A 113 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40
      removed outlier: 3.674A  pdb=" N   GLY A  66 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336
    Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 411
      removed outlier: 4.615A  pdb=" N   ARG A 409 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411
      removed outlier: 4.615A  pdb=" N   ARG A 409 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722
    Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 851
    Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 924
      removed outlier: 7.529A  pdb=" N   ILE A 908 " --> pdb=" O   MET A1027 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A1074 " --> pdb=" O   LYS A1024 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1117 through 1123
      removed outlier: 4.600A  pdb=" N   TYR A1166 " --> pdb=" O   LYS A 987 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1123
      removed outlier: 6.923A  pdb=" N   SER A 983 " --> pdb=" O   VAL A1173 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   VAL A1173 " --> pdb=" O   SER A 983 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1178 through 1180
      removed outlier: 3.918A  pdb=" N   PHE A1187 " --> pdb=" O   HIS A1190 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1338 through 1340
      removed outlier: 4.239A  pdb=" N   MET A1339 " --> pdb=" O   ARG A1422 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1488
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1496 through 1503
      removed outlier: 3.651A  pdb=" N   LEU A1502 " --> pdb=" O   ARG A1579 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ARG A1579 " --> pdb=" O   LEU A1502 " (cutoff:3.500A)

    623 hydrogen bonds defined for protein.
    1773 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 6.76

  Time building geometry restraints manager: 4.62 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: 3816
        1.33 -     1.45: 2471
        1.45 -     1.57: 7294
        1.57 -     1.69: 80
        1.69 -     1.81: 118
  Bond restraints: 13779
  Sorted by residual:
  bond pdb=" N   ASN A  14 "
       pdb=" CA  ASN A  14 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 4.01e+00
  bond pdb=" CB  ASN A 765 "
       pdb=" CG  ASN A 765 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.32e+00
  bond pdb=" CB  LYS A 997 "
       pdb=" CG  LYS A 997 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.08e+00
  bond pdb=" CG  GLN A 670 "
       pdb=" CD  GLN A 670 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 2.50e-02 1.60e+03 1.97e+00
  bond pdb=" CB  TRP A1198 "
       pdb=" CG  TRP A1198 "
    ideal  model  delta    sigma   weight residual
    1.498  1.455  0.043 3.10e-02 1.04e+03 1.94e+00
  ... (remaining 13774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 18311
        1.95 -     3.89: 432
        3.89 -     5.84: 43
        5.84 -     7.78: 16
        7.78 -     9.73: 1
  Bond angle restraints: 18803
  Sorted by residual:
  angle pdb=" N   GLU A 290 "
        pdb=" CA  GLU A 290 "
        pdb=" C   GLU A 290 "
      ideal   model   delta    sigma   weight residual
     111.02  117.20   -6.18 1.25e+00 6.40e-01 2.45e+01
  angle pdb=" C   THR A  91 "
        pdb=" CA  THR A  91 "
        pdb=" CB  THR A  91 "
      ideal   model   delta    sigma   weight residual
     115.89  109.37    6.52 1.32e+00 5.74e-01 2.44e+01
  angle pdb=" CA  TRP A 520 "
        pdb=" CB  TRP A 520 "
        pdb=" CG  TRP A 520 "
      ideal   model   delta    sigma   weight residual
     113.60  121.31   -7.71 1.90e+00 2.77e-01 1.65e+01
  angle pdb=" P     C G   4 "
        pdb=" O5'   C G   4 "
        pdb=" C5'   C G   4 "
      ideal   model   delta    sigma   weight residual
     120.90  126.80   -5.90 1.50e+00 4.44e-01 1.55e+01
  angle pdb=" N   SER A  96 "
        pdb=" CA  SER A  96 "
        pdb=" C   SER A  96 "
      ideal   model   delta    sigma   weight residual
     114.62  110.51    4.11 1.14e+00 7.69e-01 1.30e+01
  ... (remaining 18798 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.43: 8017
       33.43 -    66.85: 332
       66.85 -   100.28: 33
      100.28 -   133.71: 1
      133.71 -   167.14: 1
  Dihedral angle restraints: 8384
    sinusoidal: 3828
      harmonic: 4556
  Sorted by residual:
  dihedral pdb=" O4'   U T  22 "
           pdb=" C1'   U T  22 "
           pdb=" N1    U T  22 "
           pdb=" C2    U T  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   64.86  167.14     1      1.70e+01 3.46e-03 6.56e+01
  dihedral pdb=" CA  LEU A 546 "
           pdb=" C   LEU A 546 "
           pdb=" N   LYS A 547 "
           pdb=" CA  LYS A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" O4'   G P  16 "
           pdb=" C1'   G P  16 "
           pdb=" N9    G P  16 "
           pdb=" C4    G P  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -174.98   68.98     1      1.70e+01 3.46e-03 2.13e+01
  ... (remaining 8381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1303
       0.038 -    0.075: 594
       0.075 -    0.113: 172
       0.113 -    0.151: 41
       0.151 -    0.189: 4
  Chirality restraints: 2114
  Sorted by residual:
  chirality pdb=" CA  PRO A1007 "
            pdb=" N   PRO A1007 "
            pdb=" C   PRO A1007 "
            pdb=" CB  PRO A1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.90e-01
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" C1'   A E   5 "
            pdb=" O4'   A E   5 "
            pdb=" C2'   A E   5 "
            pdb=" N9    A E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.16 2.00e-01 2.50e+01 6.64e-01
  ... (remaining 2111 not shown)

  Planarity restraints: 2242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 639 "   -0.016 2.00e-02 2.50e+03   3.14e-02 9.86e+00
        pdb=" C   SER A 639 "    0.054 2.00e-02 2.50e+03
        pdb=" O   SER A 639 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A 640 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A1006 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.21e+00
        pdb=" N   PRO A1007 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A1007 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A1007 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 235 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO A 236 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 236 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 236 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2239 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 75
        2.55 -     3.14: 10023
        3.14 -     3.73: 20569
        3.73 -     4.31: 28616
        4.31 -     4.90: 47778
  Nonbonded interactions: 107061
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 985 "
            pdb="MG    MG A2101 "
     model   vdw
     1.964 2.170
  nonbonded pdb=" OD1 ASP A1127 "
            pdb="MG    MG A2101 "
     model   vdw
     2.033 2.170
  nonbonded pdb=" O   LYS A 798 "
            pdb=" OH  TYR A1166 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" O2'   G T  16 "
            pdb=" OP2   U T  18 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR A1110 "
            pdb=" OD1 ASP A1141 "
     model   vdw
     2.231 3.040
  ... (remaining 107056 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=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.840
  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:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     48.280
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
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      :  0.007   0.061  13779  Z= 0.298
  Angle     :  0.734   9.727  18803  Z= 0.394
  Chirality :  0.046   0.189   2114
  Planarity :  0.006   0.076   2242
  Dihedral  : 17.129 167.137   5436
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 12.63 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.20), residues: 1558
  helix:  0.46 (0.18), residues: 771
  sheet: -0.30 (0.46), residues: 137
  loop : -2.24 (0.21), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 520 
 HIS   0.007   0.001   HIS A1246 
 PHE   0.028   0.002   PHE A 649 
 TYR   0.017   0.002   TYR A 668 
 ARG   0.007   0.001   ARG A1579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14670 (  624)
  hydrogen bonds       : angle       5.25549 ( 1829)
  covalent geometry    : bond        0.00706 (13779)
  covalent geometry    : angle       0.73367 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 139
  time to evaluate  : 1.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6546 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7227 (p0) cc_final: 0.6646 (p0)
REVERT: A  543 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8695 (tp)
REVERT: A  636 LYS cc_start: 0.8476 (mttt) cc_final: 0.8226 (mtmt)
REVERT: A  851 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (p)
REVERT: A  884 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7148 (tmtt)
REVERT: A  919 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7143 (tt)
REVERT: A 1205 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8668 (pp)
REVERT: A 1215 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (mt0)
REVERT: A 1217 ASP cc_start: 0.8200 (m-30) cc_final: 0.7795 (m-30)
REVERT: A 1290 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7116 (mmp-170)
REVERT: A 1414 TYR cc_start: 0.7400 (p90) cc_final: 0.7141 (p90)
  outliers start: 88
  outliers final: 40
  residues processed: 216
  average time/residue: 1.3828
  time to fit residues: 325.8310
Evaluate side-chains
  175 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 127
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  862 SER
Chi-restraints excluded: chain A residue  865 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  884 LYS
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1122 ILE
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1205 ILE
Chi-restraints excluded: chain A residue 1215 GLN
Chi-restraints excluded: chain A residue 1248 MET
Chi-restraints excluded: chain A residue 1260 THR
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1360 ASP
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1409 VAL
Chi-restraints excluded: chain A residue 1435 LYS
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1459 ASN
Chi-restraints excluded: chain A residue 1485 THR
Chi-restraints excluded: chain A residue 1511 CYS
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1570 PHE
Chi-restraints excluded: chain A residue 1582 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 119 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 123 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9980
   chunk 143 optimal weight:    9.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
A 467 ASN
A 765 ASN
A 870 HIS
A 915 GLN
A 964 ASN
A1242 GLN
A1353 ASN
** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1599 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.142485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.108149 restraints weight = 33664.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.70
r_work: 0.3178 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13779  Z= 0.118
  Angle     :  0.556   7.177  18803  Z= 0.296
  Chirality :  0.039   0.166   2114
  Planarity :  0.004   0.069   2242
  Dihedral  : 14.771 171.414   2450
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.42 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.21), residues: 1558
  helix:  1.02 (0.19), residues: 762
  sheet:  0.37 (0.47), residues: 122
  loop : -2.09 (0.21), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 520 
 HIS   0.004   0.001   HIS A1246 
 PHE   0.019   0.001   PHE A1567 
 TYR   0.016   0.001   TYR A  28 
 ARG   0.003   0.000   ARG A1197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04737 (  624)
  hydrogen bonds       : angle       4.28385 ( 1829)
  covalent geometry    : bond        0.00252 (13779)
  covalent geometry    : angle       0.55565 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.7015 (pp) cc_final: 0.6759 (pp)
REVERT: A   93 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6527 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7249 (p0) cc_final: 0.6740 (p0)
REVERT: A  153 ILE cc_start: 0.8127 (mt) cc_final: 0.7752 (tt)
REVERT: A  183 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7751 (mp)
REVERT: A  422 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7730 (tm-30)
REVERT: A  636 LYS cc_start: 0.8608 (mttt) cc_final: 0.8298 (mtmt)
REVERT: A  689 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8046 (mptt)
REVERT: A  723 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.7018 (ppp80)
REVERT: A  919 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6869 (tm)
REVERT: A 1215 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6942 (mt0)
REVERT: A 1290 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7665 (mtp180)
REVERT: A 1422 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6692 (ptp90)
REVERT: A 1460 GLN cc_start: 0.5800 (pm20) cc_final: 0.5567 (pm20)
  outliers start: 44
  outliers final: 18
  residues processed: 175
  average time/residue: 1.2855
  time to fit residues: 245.7939
Evaluate side-chains
  152 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  723 ARG
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  865 GLN
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1215 GLN
Chi-restraints excluded: chain A residue 1260 THR
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1570 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 149 optimal weight:    2.9990
   chunk 150 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A   2 ASN
A 915 GLN
** A1467 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.139196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105701 restraints weight = 49099.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 3.57
r_work: 0.3111 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13779  Z= 0.180
  Angle     :  0.584   7.042  18803  Z= 0.311
  Chirality :  0.041   0.163   2114
  Planarity :  0.005   0.065   2242
  Dihedral  : 14.475 169.866   2398
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.56 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.21), residues: 1558
  helix:  1.06 (0.19), residues: 761
  sheet:  0.29 (0.47), residues: 122
  loop : -2.09 (0.21), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 520 
 HIS   0.005   0.001   HIS A1246 
 PHE   0.020   0.002   PHE A 649 
 TYR   0.012   0.002   TYR A1166 
 ARG   0.007   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  624)
  hydrogen bonds       : angle       4.25657 ( 1829)
  covalent geometry    : bond        0.00421 (13779)
  covalent geometry    : angle       0.58446 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 130
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6498 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7126 (p0) cc_final: 0.6614 (p0)
REVERT: A  636 LYS cc_start: 0.8654 (mttt) cc_final: 0.8341 (mtmt)
REVERT: A  689 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8210 (mmtp)
REVERT: A  919 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7231 (tt)
REVERT: A 1215 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6977 (mt0)
REVERT: A 1290 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7758 (mtp180)
REVERT: A 1416 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6664 (mt)
REVERT: A 1460 GLN cc_start: 0.5795 (pm20) cc_final: 0.5537 (pm20)
REVERT: A 1556 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7532 (tp)
  outliers start: 58
  outliers final: 25
  residues processed: 174
  average time/residue: 1.3189
  time to fit residues: 252.2070
Evaluate side-chains
  153 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  865 GLN
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1215 GLN
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1260 THR
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1416 LEU
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1565 VAL
Chi-restraints excluded: chain A residue 1570 PHE
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 155 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0170
   chunk 19 optimal weight:    8.9990
   chunk 98 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    3.4026

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
A 358 HIS
A1174 ASN
A1467 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.137802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104291 restraints weight = 41667.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 3.00
r_work: 0.3104 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13779  Z= 0.226
  Angle     :  0.632   8.168  18803  Z= 0.335
  Chirality :  0.043   0.171   2114
  Planarity :  0.005   0.067   2242
  Dihedral  : 14.480 167.495   2394
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 17.56 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.21), residues: 1558
  helix:  0.98 (0.19), residues: 760
  sheet:  0.13 (0.46), residues: 122
  loop : -2.17 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 520 
 HIS   0.006   0.001   HIS A1246 
 PHE   0.023   0.002   PHE A 649 
 TYR   0.020   0.002   TYR A1414 
 ARG   0.008   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06046 (  624)
  hydrogen bonds       : angle       4.35573 ( 1829)
  covalent geometry    : bond        0.00535 (13779)
  covalent geometry    : angle       0.63184 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 129
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.6999 (pp) cc_final: 0.6735 (pp)
REVERT: A   93 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6437 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7214 (p0) cc_final: 0.6661 (p0)
REVERT: A  143 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7235 (ttt180)
REVERT: A  543 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8652 (tp)
REVERT: A  636 LYS cc_start: 0.8673 (mttt) cc_final: 0.8380 (mtmt)
REVERT: A  689 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8216 (mmtp)
REVERT: A  919 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7321 (tt)
REVERT: A 1215 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7081 (mt0)
REVERT: A 1416 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6647 (mt)
REVERT: A 1460 GLN cc_start: 0.5909 (pm20) cc_final: 0.5581 (pm20)
  outliers start: 62
  outliers final: 32
  residues processed: 178
  average time/residue: 1.3434
  time to fit residues: 261.5465
Evaluate side-chains
  160 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  862 SER
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1204 GLN
Chi-restraints excluded: chain A residue 1215 GLN
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1260 THR
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1416 LEU
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1459 ASN
Chi-restraints excluded: chain A residue 1565 VAL
Chi-restraints excluded: chain A residue 1570 PHE
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 157 optimal weight:   10.0000
   chunk 146 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 145 optimal weight:    8.9990
   chunk 2 optimal weight:    0.1980
   chunk 57 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.143062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109844 restraints weight = 41978.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.03
r_work: 0.3184 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.078  13779  Z= 0.107
  Angle     :  0.522   8.660  18803  Z= 0.278
  Chirality :  0.038   0.190   2114
  Planarity :  0.004   0.064   2242
  Dihedral  : 14.176 173.750   2386
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.94 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.21), residues: 1558
  helix:  1.33 (0.19), residues: 766
  sheet:  0.54 (0.49), residues: 117
  loop : -2.02 (0.21), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 520 
 HIS   0.004   0.001   HIS A1246 
 PHE   0.016   0.001   PHE A 649 
 TYR   0.012   0.001   TYR A1414 
 ARG   0.003   0.000   ARG A1197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  624)
  hydrogen bonds       : angle       4.03752 ( 1829)
  covalent geometry    : bond        0.00237 (13779)
  covalent geometry    : angle       0.52208 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 1.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6610 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7186 (p0) cc_final: 0.6659 (p0)
REVERT: A  280 ASP cc_start: 0.8680 (t0) cc_final: 0.8434 (t0)
REVERT: A  636 LYS cc_start: 0.8572 (mttt) cc_final: 0.8259 (mtmt)
REVERT: A  689 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8063 (mptt)
REVERT: A  919 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7045 (tt)
REVERT: A 1290 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7521 (mmp-170)
REVERT: A 1422 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6512 (ptp90)
REVERT: A 1460 GLN cc_start: 0.6020 (pm20) cc_final: 0.5680 (pm20)
REVERT: A 1505 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.3400 (tm-30)
REVERT: A 1570 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7297 (t80)
  outliers start: 42
  outliers final: 21
  residues processed: 166
  average time/residue: 1.6481
  time to fit residues: 298.8560
Evaluate side-chains
  151 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1250 LEU
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1570 PHE
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9990
   chunk 140 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 358 HIS
A 526 GLN
A 915 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.143029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109552 restraints weight = 42830.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 3.16
r_work: 0.3179 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  13779  Z= 0.108
  Angle     :  0.518   8.998  18803  Z= 0.274
  Chirality :  0.038   0.165   2114
  Planarity :  0.004   0.059   2242
  Dihedral  : 14.069 173.263   2382
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.45 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1558
  helix:  1.49 (0.19), residues: 767
  sheet:  0.72 (0.49), residues: 117
  loop : -1.99 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 520 
 HIS   0.005   0.001   HIS A1246 
 PHE   0.026   0.001   PHE A1567 
 TYR   0.018   0.001   TYR A 142 
 ARG   0.007   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  624)
  hydrogen bonds       : angle       3.94500 ( 1829)
  covalent geometry    : bond        0.00243 (13779)
  covalent geometry    : angle       0.51843 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 2.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7386 (t)
REVERT: A   93 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6679 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7177 (p0) cc_final: 0.6633 (p0)
REVERT: A  280 ASP cc_start: 0.8697 (t0) cc_final: 0.8436 (t0)
REVERT: A  636 LYS cc_start: 0.8566 (mttt) cc_final: 0.8259 (mtmt)
REVERT: A  689 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8035 (mptt)
REVERT: A  919 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7103 (tt)
REVERT: A 1290 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7514 (mmp-170)
REVERT: A 1422 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6305 (ptp90)
REVERT: A 1447 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7429 (tp)
REVERT: A 1460 GLN cc_start: 0.5953 (pm20) cc_final: 0.5587 (pm20)
REVERT: A 1505 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.3497 (tm-30)
REVERT: A 1519 GLU cc_start: 0.7711 (tp30) cc_final: 0.7354 (tp30)
  outliers start: 41
  outliers final: 18
  residues processed: 170
  average time/residue: 1.9879
  time to fit residues: 372.3094
Evaluate side-chains
  156 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 3.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  905 CYS
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 156 optimal weight:    7.9990
   chunk 130 optimal weight:   10.0000
   chunk 143 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 118 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 78 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN
A 954 ASN
** A1080 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.138854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.105103 restraints weight = 51638.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.90
r_work: 0.3084 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  13779  Z= 0.224
  Angle     :  0.629   8.580  18803  Z= 0.331
  Chirality :  0.043   0.212   2114
  Planarity :  0.005   0.061   2242
  Dihedral  : 14.131 168.777   2377
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.59 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.21), residues: 1558
  helix:  1.21 (0.19), residues: 768
  sheet:  0.11 (0.45), residues: 135
  loop : -2.01 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1538 
 HIS   0.005   0.001   HIS A1246 
 PHE   0.022   0.002   PHE A 649 
 TYR   0.021   0.002   TYR A 142 
 ARG   0.007   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05763 (  624)
  hydrogen bonds       : angle       4.19594 ( 1829)
  covalent geometry    : bond        0.00533 (13779)
  covalent geometry    : angle       0.62943 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 126
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6664 (mtm-85)
REVERT: A  134 ASN cc_start: 0.7127 (p0) cc_final: 0.6571 (p0)
REVERT: A  636 LYS cc_start: 0.8656 (mttt) cc_final: 0.8341 (mtmt)
REVERT: A  689 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8088 (mptt)
REVERT: A  919 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7262 (tt)
REVERT: A 1290 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7578 (mmp-170)
REVERT: A 1447 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7484 (tp)
REVERT: A 1460 GLN cc_start: 0.6005 (pm20) cc_final: 0.5584 (pm20)
REVERT: A 1505 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.3309 (tm-30)
  outliers start: 46
  outliers final: 25
  residues processed: 164
  average time/residue: 2.2220
  time to fit residues: 398.0587
Evaluate side-chains
  156 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 2.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1409 VAL
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1459 ASN
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1511 CYS
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 66 optimal weight:    0.0170
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 150 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 103 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 148 optimal weight:    0.9990
   overall best weight:    0.7622

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.143163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109081 restraints weight = 48911.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.48
r_work: 0.3151 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.102  13779  Z= 0.110
  Angle     :  0.535   9.398  18803  Z= 0.282
  Chirality :  0.039   0.178   2114
  Planarity :  0.004   0.062   2242
  Dihedral  : 13.977 173.490   2377
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.10 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.22), residues: 1558
  helix:  1.48 (0.19), residues: 767
  sheet:  0.30 (0.46), residues: 135
  loop : -1.93 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 520 
 HIS   0.004   0.001   HIS A1246 
 PHE   0.028   0.001   PHE A1567 
 TYR   0.016   0.001   TYR A1110 
 ARG   0.007   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  624)
  hydrogen bonds       : angle       3.97225 ( 1829)
  covalent geometry    : bond        0.00253 (13779)
  covalent geometry    : angle       0.53500 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 133
  time to evaluate  : 2.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6715 (mtm-85)
REVERT: A  280 ASP cc_start: 0.8742 (t0) cc_final: 0.8491 (t0)
REVERT: A  422 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: A  443 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8096 (tm-30)
REVERT: A  636 LYS cc_start: 0.8577 (mttt) cc_final: 0.8260 (mtmt)
REVERT: A  689 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8038 (mptt)
REVERT: A  919 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7073 (tt)
REVERT: A 1290 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7565 (mmp-170)
REVERT: A 1416 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6566 (mt)
REVERT: A 1422 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6259 (ptp90)
REVERT: A 1447 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7424 (tp)
REVERT: A 1505 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.3438 (tm-30)
  outliers start: 44
  outliers final: 21
  residues processed: 167
  average time/residue: 1.6703
  time to fit residues: 303.7159
Evaluate side-chains
  157 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 2.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1409 VAL
Chi-restraints excluded: chain A residue 1416 LEU
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   chunk 147 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 136 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    2.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.140105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.105872 restraints weight = 49986.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.63
r_work: 0.3096 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13779  Z= 0.172
  Angle     :  0.591   8.990  18803  Z= 0.311
  Chirality :  0.041   0.216   2114
  Planarity :  0.004   0.059   2242
  Dihedral  : 14.019 170.618   2377
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.04 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.21), residues: 1558
  helix:  1.35 (0.19), residues: 767
  sheet:  0.20 (0.45), residues: 135
  loop : -1.94 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A1538 
 HIS   0.004   0.001   HIS A1246 
 PHE   0.019   0.002   PHE A 649 
 TYR   0.020   0.002   TYR A 142 
 ARG   0.008   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05094 (  624)
  hydrogen bonds       : angle       4.09982 ( 1829)
  covalent geometry    : bond        0.00409 (13779)
  covalent geometry    : angle       0.59115 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 1.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.7004 (pp) cc_final: 0.6742 (pp)
REVERT: A   93 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6733 (mtm-85)
REVERT: A  135 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7709 (mp)
REVERT: A  443 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8202 (tm-30)
REVERT: A  636 LYS cc_start: 0.8624 (mttt) cc_final: 0.8309 (mtmt)
REVERT: A  689 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8077 (mptt)
REVERT: A  919 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7250 (tt)
REVERT: A 1290 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7607 (mmp-170)
REVERT: A 1304 ARG cc_start: 0.6210 (tpt170) cc_final: 0.5873 (tpt170)
REVERT: A 1447 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7453 (tp)
REVERT: A 1460 GLN cc_start: 0.5992 (pm20) cc_final: 0.5717 (pm20)
REVERT: A 1505 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.3435 (tm-30)
  outliers start: 36
  outliers final: 22
  residues processed: 155
  average time/residue: 1.4544
  time to fit residues: 245.6980
Evaluate side-chains
  156 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1409 VAL
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 132 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 142 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 133 optimal weight:    8.9990
   chunk 96 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.143227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109276 restraints weight = 36490.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.75
r_work: 0.3194 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  13779  Z= 0.113
  Angle     :  0.544   9.340  18803  Z= 0.286
  Chirality :  0.039   0.189   2114
  Planarity :  0.004   0.061   2242
  Dihedral  : 13.912 173.608   2377
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.19 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.22), residues: 1558
  helix:  1.47 (0.19), residues: 769
  sheet:  0.39 (0.46), residues: 135
  loop : -1.87 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1538 
 HIS   0.004   0.001   HIS A1246 
 PHE   0.031   0.001   PHE A1567 
 TYR   0.018   0.001   TYR A1414 
 ARG   0.008   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  624)
  hydrogen bonds       : angle       3.97825 ( 1829)
  covalent geometry    : bond        0.00262 (13779)
  covalent geometry    : angle       0.54385 (18803)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7435 (t)
REVERT: A   93 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6722 (mtm-85)
REVERT: A  155 ARG cc_start: 0.7473 (ttm110) cc_final: 0.6815 (mtp-110)
REVERT: A  280 ASP cc_start: 0.8685 (t0) cc_final: 0.8447 (t0)
REVERT: A  443 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8035 (tm-30)
REVERT: A  636 LYS cc_start: 0.8520 (mttt) cc_final: 0.8215 (mtmt)
REVERT: A  689 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8060 (mptt)
REVERT: A  919 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7083 (tt)
REVERT: A 1290 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7528 (mmp-170)
REVERT: A 1304 ARG cc_start: 0.6070 (tpt170) cc_final: 0.5778 (tpt170)
REVERT: A 1422 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6161 (ptp90)
REVERT: A 1447 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7436 (tp)
REVERT: A 1505 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.3467 (tm-30)
  outliers start: 33
  outliers final: 21
  residues processed: 161
  average time/residue: 1.4303
  time to fit residues: 250.1258
Evaluate side-chains
  160 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  905 CYS
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1050 GLU
Chi-restraints excluded: chain A residue 1120 ASP
Chi-restraints excluded: chain A residue 1143 VAL
Chi-restraints excluded: chain A residue 1290 ARG
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1364 GLN
Chi-restraints excluded: chain A residue 1371 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1409 VAL
Chi-restraints excluded: chain A residue 1422 ARG
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1505 GLU
Chi-restraints excluded: chain A residue 1596 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 152 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 131 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 153 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.110153 restraints weight = 43818.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.20
r_work: 0.3177 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  13779  Z= 0.110
  Angle     :  0.537   9.327  18803  Z= 0.284
  Chirality :  0.038   0.155   2114
  Planarity :  0.004   0.059   2242
  Dihedral  : 13.838 173.661   2377
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.48 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.22), residues: 1558
  helix:  1.60 (0.19), residues: 763
  sheet:  0.57 (0.47), residues: 135
  loop : -1.82 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A1538 
 HIS   0.005   0.001   HIS A1246 
 PHE   0.019   0.001   PHE A 934 
 TYR   0.025   0.001   TYR A1110 
 ARG   0.008   0.000   ARG A1557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  624)
  hydrogen bonds       : angle       3.92711 ( 1829)
  covalent geometry    : bond        0.00257 (13779)
  covalent geometry    : angle       0.53734 (18803)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10109.12 seconds
wall clock time: 185 minutes 37.00 seconds (11137.00 seconds total)