Starting phenix.real_space_refine
on Fri Sep 27 05:03:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/09_2024/6l42_0828.cif"
  }
  resolution = 3.4
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      91      5.16       5
     C    9388      2.51       5
     N    2574      2.21       5
     O    2773      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 14827
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 14826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1864, 14826
          Classifications: {'peptide': 1864}
          Link IDs: {'CIS': 2, 'PTRANS': 66, 'TRANS': 1795}
          Chain breaks: 15
    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: 8.02, per 1000 atoms: 0.54
  Number of scatterers: 14827
  At special positions: 0
  Unit cell: (90.72, 112.32, 138.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      91     16.00
     Mg      1     11.99
     O    2773      8.00
     N    2574      7.00
     C    9388      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: 3.80
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3488

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 14 sheets defined
      42.2% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 10
      removed outlier: 4.038A  pdb=" N   ILE A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 83
      removed outlier: 4.484A  pdb=" N   THR A  83 " --> pdb=" O   ASN A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 158
      removed outlier: 3.780A  pdb=" N   ILE A 146 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   ASP A 151 " --> pdb=" O   GLU A 147 " (cutoff:3.500A)
      Proline residue:  A 152  - end of helix
      removed outlier: 3.515A  pdb=" N   ASP A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 206
      removed outlier: 3.798A  pdb=" N   ALA A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 189 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   MET A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS A 204 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 232
      removed outlier: 4.224A  pdb=" N   ARG A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 245
    Processing helix  chain 'A' and resid 251 through 258
      removed outlier: 3.630A  pdb=" N   GLN A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 285
      removed outlier: 3.852A  pdb=" N   LYS A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 318
      removed outlier: 3.739A  pdb=" N   GLU A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE A 299 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ASN A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ARG A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 375
      removed outlier: 3.637A  pdb=" N   TRP A 365 " --> pdb=" O   TYR A 361 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LEU A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   GLY A 375 " --> pdb=" O   ASP A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.571A  pdb=" N   ILE A 406 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
      removed outlier: 4.037A  pdb=" N   LEU A 425 " --> pdb=" O   GLN A 421 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN A 426 " --> pdb=" O   GLU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 4.044A  pdb=" N   GLY A 460 " --> pdb=" O   VAL A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.992A  pdb=" N   ALA A 482 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 492
      removed outlier: 3.725A  pdb=" N   LEU A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 506 through 511
    Processing helix  chain 'A' and resid 514 through 531
      removed outlier: 4.138A  pdb=" N   TRP A 520 " --> pdb=" O   GLN A 516 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A 521 " --> pdb=" O   TRP A 517 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A 530 " --> pdb=" O   GLN A 526 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 531 " --> pdb=" O   GLU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 611
      removed outlier: 4.379A  pdb=" N   LEU A 609 " --> pdb=" O   LYS A 605 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASN A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 615
    Processing helix  chain 'A' and resid 616 through 621
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 638 through 652
      removed outlier: 3.846A  pdb=" N   GLU A 643 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLN A 644 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 648 " --> pdb=" O   GLN A 644 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 650 " --> pdb=" O   GLY A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 661
      removed outlier: 3.951A  pdb=" N   GLU A 660 " --> pdb=" O   LYS A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 667
    Processing helix  chain 'A' and resid 670 through 675
      removed outlier: 3.623A  pdb=" N   VAL A 675 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 690
      removed outlier: 3.567A  pdb=" N   LEU A 687 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLY A 688 " --> pdb=" O   LYS A 685 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LYS A 689 " --> pdb=" O   MET A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 713
      removed outlier: 3.581A  pdb=" N   TYR A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ASP A 708 " --> pdb=" O   ARG A 704 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   CYS A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   MET A 710 " --> pdb=" O   HIS A 706 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   VAL A 711 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE A 713 " --> pdb=" O   CYS A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 750
      removed outlier: 4.419A  pdb=" N   ASN A 748 " --> pdb=" O   GLU A 744 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER A 749 " --> pdb=" O   ASN A 745 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TRP A 750 " --> pdb=" O   MET A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 776
      removed outlier: 3.521A  pdb=" N   LEU A 767 " --> pdb=" O   GLU A 763 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU A 769 " --> pdb=" O   ASN A 765 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ILE A 774 " --> pdb=" O   MET A 770 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 775 " --> pdb=" O   TYR A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 819
      removed outlier: 3.546A  pdb=" N   LEU A 806 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER A 812 " --> pdb=" O   ALA A 808 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU A 813 " --> pdb=" O   ALA A 809 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLU A 814 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ARG A 815 " --> pdb=" O   SER A 811 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA A 818 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 838
      removed outlier: 4.610A  pdb=" N   GLU A 831 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A 835 " --> pdb=" O   GLU A 831 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   GLY A 838 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 859
      removed outlier: 3.536A  pdb=" N   GLU A 859 " --> pdb=" O   LYS A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 883
      removed outlier: 3.579A  pdb=" N   LEU A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 902
    Processing helix  chain 'A' and resid 929 through 945
      removed outlier: 3.959A  pdb=" N   VAL A 936 " --> pdb=" O   VAL A 932 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR A 938 " --> pdb=" O   PHE A 934 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   MET A 939 " --> pdb=" O   GLY A 935 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   VAL A 943 " --> pdb=" O   MET A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 960
    Processing helix  chain 'A' and resid 961 through 969
      removed outlier: 4.294A  pdb=" N   GLY A 966 " --> pdb=" O   ILE A 962 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   LEU A 967 " --> pdb=" O   GLU A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1006
      removed outlier: 4.357A  pdb=" N   LEU A 998 " --> pdb=" O   TYR A 994 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A 999 " --> pdb=" O   THR A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1019
      removed outlier: 4.181A  pdb=" N   ALA A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1037
      removed outlier: 3.667A  pdb=" N   LEU A1033 " --> pdb=" O   ASP A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1058
    Processing helix  chain 'A' and resid 1086 through 1107
      removed outlier: 3.562A  pdb=" N   LEU A1090 " --> pdb=" O   THR A1086 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER A1104 " --> pdb=" O   SER A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1155
      removed outlier: 3.583A  pdb=" N   PHE A1147 " --> pdb=" O   VAL A1143 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   PHE A1148 " --> pdb=" O   ARG A1144 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A1152 " --> pdb=" O   PHE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1158
      No H-bonds generated for 'chain 'A' and resid 1156 through 1158'
    Processing helix  chain 'A' and resid 1195 through 1200
      removed outlier: 3.742A  pdb=" N   ALA A1200 " --> pdb=" O   LEU A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1212 through 1228
      removed outlier: 3.767A  pdb=" N   GLU A1216 " --> pdb=" O   ALA A1212 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN A1224 " --> pdb=" O   ASN A1220 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   CYS A1225 " --> pdb=" O   LEU A1221 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A1226 " --> pdb=" O   LEU A1222 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU A1227 " --> pdb=" O   THR A1223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1252
      removed outlier: 3.610A  pdb=" N   LEU A1244 " --> pdb=" O   CYS A1240 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU A1249 " --> pdb=" O   HIS A1245 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A1250 " --> pdb=" O   HIS A1246 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A1251 " --> pdb=" O   TYR A1247 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU A1252 " --> pdb=" O   MET A1248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1266
      removed outlier: 3.802A  pdb=" N   LEU A1265 " --> pdb=" O   PHE A1261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1288 through 1299
      removed outlier: 3.721A  pdb=" N   ASN A1292 " --> pdb=" O   GLY A1288 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A1299 " --> pdb=" O   ARG A1295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1311
    Processing helix  chain 'A' and resid 1345 through 1350
    Processing helix  chain 'A' and resid 1360 through 1367
    Processing helix  chain 'A' and resid 1369 through 1373
      removed outlier: 3.570A  pdb=" N   TYR A1373 " --> pdb=" O   GLY A1370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1378 through 1392
      removed outlier: 3.683A  pdb=" N   HIS A1391 " --> pdb=" O   ALA A1387 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   SER A1392 " --> pdb=" O   GLU A1388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1418
      removed outlier: 3.766A  pdb=" N   ARG A1407 " --> pdb=" O   HIS A1403 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A1409 " --> pdb=" O   VAL A1405 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA A1411 " --> pdb=" O   ARG A1407 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LEU A1415 " --> pdb=" O   ALA A1411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1435 through 1443
      removed outlier: 3.513A  pdb=" N   ILE A1439 " --> pdb=" O   LYS A1435 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A1440 " --> pdb=" O   ALA A1436 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A1441 " --> pdb=" O   SER A1437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1451 through 1457
    Processing helix  chain 'A' and resid 1514 through 1522
      removed outlier: 4.108A  pdb=" N   SER A1518 " --> pdb=" O   GLU A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1536 through 1544
      removed outlier: 3.695A  pdb=" N   LYS A1540 " --> pdb=" O   GLU A1536 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER A1544 " --> pdb=" O   LYS A1540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 3.614A  pdb=" N   ARG A1557 " --> pdb=" O   SER A1553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1563 through 1572
      removed outlier: 3.616A  pdb=" N   PHE A1567 " --> pdb=" O   SER A1563 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASN A1569 " --> pdb=" O   VAL A1565 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   PHE A1570 " --> pdb=" O   GLN A1566 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A1571 " --> pdb=" O   PHE A1567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1617 through 1628
    Processing helix  chain 'A' and resid 1635 through 1638
    Processing helix  chain 'A' and resid 1639 through 1647
      removed outlier: 3.744A  pdb=" N   GLU A1643 " --> pdb=" O   GLY A1639 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU A1644 " --> pdb=" O   PRO A1640 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   TYR A1645 " --> pdb=" O   TYR A1641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1671 through 1676
    Processing helix  chain 'A' and resid 1688 through 1694
      removed outlier: 3.883A  pdb=" N   ILE A1692 " --> pdb=" O   ILE A1688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1758 through 1773
      removed outlier: 3.956A  pdb=" N   GLU A1763 " --> pdb=" O   TYR A1759 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A1768 " --> pdb=" O   SER A1764 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP A1770 " --> pdb=" O   ARG A1766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1797 through 1801
    Processing helix  chain 'A' and resid 1859 through 1866
      removed outlier: 3.631A  pdb=" N   ALA A1863 " --> pdb=" O   GLU A1859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1871 through 1875
    Processing helix  chain 'A' and resid 1900 through 1909
      removed outlier: 3.614A  pdb=" N   ASP A1904 " --> pdb=" O   LEU A1900 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A1905 " --> pdb=" O   LEU A1901 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LYS A1906 " --> pdb=" O   ALA A1902 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLN A1908 " --> pdb=" O   ASP A1904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1922 through 1924
      No H-bonds generated for 'chain 'A' and resid 1922 through 1924'
    Processing helix  chain 'A' and resid 1925 through 1933
      removed outlier: 4.243A  pdb=" N   LYS A1929 " --> pdb=" O   GLY A1925 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A1932 " --> pdb=" O   ARG A1928 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   MET A1933 " --> pdb=" O   LYS A1929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1936 through 1941
      removed outlier: 3.666A  pdb=" N   MET A1940 " --> pdb=" O   LYS A1936 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL A1941 " --> pdb=" O   LEU A1937 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1936 through 1941'
    Processing helix  chain 'A' and resid 2012 through 2019
      removed outlier: 3.663A  pdb=" N   ASP A2016 " --> pdb=" O   LEU A2012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2029 through 2034
    Processing helix  chain 'A' and resid 2041 through 2049
      removed outlier: 3.880A  pdb=" N   GLN A2047 " --> pdb=" O   ALA A2043 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17
      removed outlier: 6.076A  pdb=" N   GLY A  15 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   PHE A 167 " --> pdb=" O   GLY A  15 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   SER A  17 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   VAL A 169 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 6.076A  pdb=" N   GLY A  15 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   PHE A 167 " --> pdb=" O   GLY A  15 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   SER A  17 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   VAL A 169 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE A 122 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   GLY A 168 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   VAL A 124 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   GLU A 126 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 8.373A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 113 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.502A  pdb=" N   ILE A 570 " --> pdb=" O   GLU A 594 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A 594 " --> pdb=" O   ILE A 570 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 595 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 566
    Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 721
      removed outlier: 3.510A  pdb=" N   ILE A 721 " --> pdb=" O   GLU A 728 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU A 728 " --> pdb=" O   ILE A 721 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 923
      removed outlier: 4.393A  pdb=" N   LEU A 910 " --> pdb=" O   MET A1027 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A1024 " --> pdb=" O   THR A1074 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 980 through 981
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1179 through 1180
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1328 through 1330
      removed outlier: 3.816A  pdb=" N   ALA A1328 " --> pdb=" O   SER A1335 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1699 through 1700
      removed outlier: 3.709A  pdb=" N   LEU A1700 " --> pdb=" O   VAL A1728 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1709 through 1712
      removed outlier: 3.912A  pdb=" N   GLY A1716 " --> pdb=" O   ARG A1712 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1726
      removed outlier: 6.589A  pdb=" N   GLN A1735 " --> pdb=" O   ILE A1750 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ILE A1750 " --> pdb=" O   GLN A1735 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU A1737 " --> pdb=" O   GLU A1748 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1825 through 1829
      removed outlier: 3.860A  pdb=" N   ARG A1829 " --> pdb=" O   ILE A1832 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A1832 " --> pdb=" O   ARG A1829 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LEU A1833 " --> pdb=" O   SER A1849 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   SER A1849 " --> pdb=" O   LEU A1833 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU A1835 " --> pdb=" O   ILE A1847 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A1847 " --> pdb=" O   LEU A1835 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ARG A1843 " --> pdb=" O   ILE A1839 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1122 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.69

  Time building geometry restraints manager: 4.42 seconds

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

  Histogram of bond lengths:
        1.00 -     1.16: 4
        1.16 -     1.33: 2757
        1.33 -     1.49: 5739
        1.49 -     1.65: 6461
        1.65 -     1.81: 156
  Bond restraints: 15117
  Sorted by residual:
  bond pdb=" CA  VAL A1520 "
       pdb=" C   VAL A1520 "
    ideal  model  delta    sigma   weight residual
    1.522  1.174  0.348 1.50e-02 4.44e+03 5.39e+02
  bond pdb=" C   ALA A 892 "
       pdb=" N   VAL A 893 "
    ideal  model  delta    sigma   weight residual
    1.336  1.591 -0.255 1.17e-02 7.31e+03 4.75e+02
  bond pdb=" C   THR A 348 "
       pdb=" N   ASP A 349 "
    ideal  model  delta    sigma   weight residual
    1.333  1.596 -0.262 1.34e-02 5.57e+03 3.83e+02
  bond pdb=" CA  THR A 348 "
       pdb=" C   THR A 348 "
    ideal  model  delta    sigma   weight residual
    1.533  1.638 -0.104 5.60e-03 3.19e+04 3.48e+02
  bond pdb=" C   MET A   1 "
       pdb=" N   ASN A   2 "
    ideal  model  delta    sigma   weight residual
    1.332  1.576 -0.243 1.40e-02 5.10e+03 3.02e+02
  ... (remaining 15112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.12: 19984
       10.12 -    20.23: 260
       20.23 -    30.35: 76
       30.35 -    40.47: 47
       40.47 -    50.59: 12
  Bond angle restraints: 20379
  Sorted by residual:
  angle pdb=" O   THR A 348 "
        pdb=" C   THR A 348 "
        pdb=" N   ASP A 349 "
      ideal   model   delta    sigma   weight residual
     121.47   79.92   41.55 7.50e-01 1.78e+00 3.07e+03
  angle pdb=" CA  THR A 348 "
        pdb=" C   THR A 348 "
        pdb=" N   ASP A 349 "
      ideal   model   delta    sigma   weight residual
     120.47  157.47  -37.00 1.03e+00 9.43e-01 1.29e+03
  angle pdb=" O   SER A1580 "
        pdb=" C   SER A1580 "
        pdb=" N   VAL A1581 "
      ideal   model   delta    sigma   weight residual
     122.97   78.20   44.77 1.39e+00 5.18e-01 1.04e+03
  angle pdb=" O   LEU A1584 "
        pdb=" C   LEU A1584 "
        pdb=" N   GLY A1585 "
      ideal   model   delta    sigma   weight residual
     123.13   89.16   33.97 1.07e+00 8.73e-01 1.01e+03
  angle pdb=" O   VAL A1581 "
        pdb=" C   VAL A1581 "
        pdb=" N   ARG A1582 "
      ideal   model   delta    sigma   weight residual
     122.57  161.28  -38.71 1.25e+00 6.40e-01 9.59e+02
  ... (remaining 20374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.74: 8465
       25.74 -    51.48: 611
       51.48 -    77.23: 65
       77.23 -   102.97: 10
      102.97 -   128.71: 2
  Dihedral angle restraints: 9153
    sinusoidal: 3763
      harmonic: 5390
  Sorted by residual:
  dihedral pdb=" CA  THR A 348 "
           pdb=" C   THR A 348 "
           pdb=" N   ASP A 349 "
           pdb=" CA  ASP A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -51.29 -128.71     0      5.00e+00 4.00e-02 6.63e+02
  dihedral pdb=" CA  VAL A1574 "
           pdb=" C   VAL A1574 "
           pdb=" N   ASP A1575 "
           pdb=" CA  ASP A1575 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   65.64  114.36     0      5.00e+00 4.00e-02 5.23e+02
  dihedral pdb=" CA  LEU A  95 "
           pdb=" C   LEU A  95 "
           pdb=" N   SER A  96 "
           pdb=" CA  SER A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   87.25   92.75     0      5.00e+00 4.00e-02 3.44e+02
  ... (remaining 9150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.310: 2134
       0.310 -    0.620: 92
       0.620 -    0.930: 16
       0.930 -    1.240: 4
       1.240 -    1.550: 10
  Chirality restraints: 2256
  Sorted by residual:
  chirality pdb=" CA  PHE A1793 "
            pdb=" N   PHE A1793 "
            pdb=" C   PHE A1793 "
            pdb=" CB  PHE A1793 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.96    1.55 2.00e-01 2.50e+01 6.01e+01
  chirality pdb=" CA  TRP A 790 "
            pdb=" N   TRP A 790 "
            pdb=" C   TRP A 790 "
            pdb=" CB  TRP A 790 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.98    1.53 2.00e-01 2.50e+01 5.83e+01
  chirality pdb=" CA  GLN A 824 "
            pdb=" N   GLN A 824 "
            pdb=" C   GLN A 824 "
            pdb=" CB  GLN A 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.99    1.52 2.00e-01 2.50e+01 5.80e+01
  ... (remaining 2253 not shown)

  Planarity restraints: 2599
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A1393 "   -0.153 2.00e-02 2.50e+03   3.09e-01 9.54e+02
        pdb=" C   PRO A1393 "    0.522 2.00e-02 2.50e+03
        pdb=" O   PRO A1393 "   -0.280 2.00e-02 2.50e+03
        pdb=" N   GLY A1394 "   -0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1687 "   -0.158 2.00e-02 2.50e+03   2.47e-01 6.11e+02
        pdb=" C   SER A1687 "    0.422 2.00e-02 2.50e+03
        pdb=" O   SER A1687 "   -0.187 2.00e-02 2.50e+03
        pdb=" N   ILE A1688 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1584 "   -0.141 2.00e-02 2.50e+03   2.43e-01 5.92e+02
        pdb=" C   LEU A1584 "    0.418 2.00e-02 2.50e+03
        pdb=" O   LEU A1584 "   -0.180 2.00e-02 2.50e+03
        pdb=" N   GLY A1585 "   -0.097 2.00e-02 2.50e+03
  ... (remaining 2596 not shown)

  Histogram of nonbonded interaction distances:
        1.22 -     1.96: 55
        1.96 -     2.69: 1041
        2.69 -     3.43: 21036
        3.43 -     4.16: 32655
        4.16 -     4.90: 56204
  Nonbonded interactions: 110991
  Sorted by model distance:
  nonbonded pdb=" CZ  PHE A1567 "
            pdb=" CD1 ILE A1571 "
     model   vdw
     1.223 3.760
  nonbonded pdb=" O   ASP A1515 "
            pdb=" OE1 GLU A1519 "
     model   vdw
     1.260 3.040
  nonbonded pdb=" O   PHE A  84 "
            pdb=" OG  SER A  88 "
     model   vdw
     1.354 3.040
  nonbonded pdb=" CB  ALA A1296 "
            pdb=" OD2 ASP A1301 "
     model   vdw
     1.363 3.460
  nonbonded pdb=" CE2 TYR A1348 "
            pdb=" CB  SER A1397 "
     model   vdw
     1.393 3.740
  ... (remaining 110986 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     35.090
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.070
  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:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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      :  0.013   0.348  15117  Z= 0.808
  Angle     :  3.318  50.587  20379  Z= 2.152
  Chirality :  0.171   1.550   2256
  Planarity :  0.021   0.309   2599
  Dihedral  : 16.555 128.708   5665
  Min Nonbonded Distance : 1.223

Molprobity Statistics.
  All-atom Clashscore : 41.56
  Ramachandran Plot:
    Outliers :  2.02 %
    Allowed  : 11.41 %
    Favored  : 86.57 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  :  7.40 %
    Favored  : 85.99 %
  Cbeta Deviations :  6.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 1.80 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.16 (0.15), residues: 1832
  helix: -3.17 (0.14), residues: 663
  sheet: -2.42 (0.41), residues: 136
  loop : -3.92 (0.16), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 520 
 HIS   0.004   0.001   HIS A 916 
 PHE   0.127   0.002   PHE A 352 
 TYR   0.010   0.001   TYR A1101 
 ARG   0.013   0.000   ARG A1568 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  442 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 108
    poor density    : 334
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.7288 (tt0) cc_final: 0.7047 (mt-10)
REVERT: A  420 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7575 (mtp-110)
REVERT: A  672 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10)
REVERT: A  773 LYS cc_start: 0.9095 (tttt) cc_final: 0.8802 (ttmm)
REVERT: A  777 MET cc_start: 0.8179 (ttm) cc_final: 0.7872 (ttm)
REVERT: A  778 GLU cc_start: 0.8119 (tp30) cc_final: 0.7882 (tp30)
REVERT: A  913 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7176 (ptmt)
REVERT: A  933 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8491 (tm-30)
REVERT: A 1020 MET cc_start: 0.8014 (mtp) cc_final: 0.7746 (mtm)
REVERT: A 1067 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8154 (tppt)
REVERT: A 1131 MET cc_start: 0.7983 (mtm) cc_final: 0.7644 (mtt)
REVERT: A 1527 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.5840 (m)
REVERT: A 1544 SER cc_start: 0.5449 (OUTLIER) cc_final: 0.5127 (p)
REVERT: A 1637 LEU cc_start: 0.9154 (pp) cc_final: 0.8943 (pp)
REVERT: A 1791 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7722 (p)
REVERT: A 1800 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7671 (ttm-80)
REVERT: A 2015 MET cc_start: 0.8374 (tpp) cc_final: 0.8097 (tpt)
  outliers start: 108
  outliers final: 53
  residues processed: 415
  average time/residue: 0.3448
  time to fit residues: 195.6726
Evaluate side-chains
  281 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 223
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  161 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  888 TRP
Chi-restraints excluded: chain A residue  913 LYS
Chi-restraints excluded: chain A residue  921 GLU
Chi-restraints excluded: chain A residue  949 HIS
Chi-restraints excluded: chain A residue  971 ARG
Chi-restraints excluded: chain A residue 1024 LYS
Chi-restraints excluded: chain A residue 1064 TRP
Chi-restraints excluded: chain A residue 1067 LYS
Chi-restraints excluded: chain A residue 1071 TYR
Chi-restraints excluded: chain A residue 1107 LYS
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1460 GLN
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1521 TRP
Chi-restraints excluded: chain A residue 1527 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1537 GLU
Chi-restraints excluded: chain A residue 1538 TRP
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1542 ARG
Chi-restraints excluded: chain A residue 1544 SER
Chi-restraints excluded: chain A residue 1545 PHE
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1649 MET
Chi-restraints excluded: chain A residue 1652 GLU
Chi-restraints excluded: chain A residue 1657 LEU
Chi-restraints excluded: chain A residue 1790 LEU
Chi-restraints excluded: chain A residue 1791 SER
Chi-restraints excluded: chain A residue 1796 LYS
Chi-restraints excluded: chain A residue 1810 GLU
Chi-restraints excluded: chain A residue 1911 ASP
Chi-restraints excluded: chain A residue 1976 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    9.9990
   chunk 140 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 145 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 168 optimal weight:   10.0000
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 185 GLN
A 237 ASN
A 376 ASN
A 466 ASN
A 513 ASN
A 618 ASN
A 841 ASN
A 915 GLN
A 964 ASN
A1011 HIS
A1035 HIS
A1190 HIS
A1204 GLN
A1239 GLN
A1930 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  15117  Z= 0.314
  Angle     :  0.917  13.182  20379  Z= 0.479
  Chirality :  0.051   0.257   2256
  Planarity :  0.007   0.097   2599
  Dihedral  : 10.832  76.801   2165
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 11.52 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.17 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.67 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.17), residues: 1832
  helix: -2.27 (0.17), residues: 708
  sheet: -1.76 (0.42), residues: 141
  loop : -3.66 (0.17), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 520 
 HIS   0.012   0.001   HIS A 916 
 PHE   0.020   0.002   PHE A  84 
 TYR   0.025   0.002   TYR A1348 
 ARG   0.010   0.001   ARG A 871 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 243
  time to evaluate  : 1.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.7428 (tt0) cc_final: 0.7141 (mt-10)
REVERT: A  406 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7082 (pt)
REVERT: A  773 LYS cc_start: 0.9136 (tttt) cc_final: 0.8886 (ttmm)
REVERT: A  888 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.8219 (m-10)
REVERT: A  913 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7670 (ptmt)
REVERT: A  971 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (ttm110)
REVERT: A 1020 MET cc_start: 0.8184 (mtp) cc_final: 0.7923 (mtm)
REVERT: A 1111 MET cc_start: 0.8807 (mpp) cc_final: 0.8198 (ppp)
REVERT: A 1131 MET cc_start: 0.7991 (mtm) cc_final: 0.7631 (mtt)
REVERT: A 1463 MET cc_start: 0.3181 (ttm) cc_final: 0.2448 (tmm)
REVERT: A 1527 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6659 (m)
REVERT: A 1532 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8227 (mmm-85)
REVERT: A 1556 LEU cc_start: 0.8186 (tp) cc_final: 0.7883 (mp)
REVERT: A 1564 HIS cc_start: 0.5582 (m-70) cc_final: 0.5012 (m-70)
REVERT: A 1620 GLN cc_start: 0.9483 (tp40) cc_final: 0.9228 (tp-100)
REVERT: A 1746 TRP cc_start: 0.8685 (p90) cc_final: 0.7860 (p90)
REVERT: A 1800 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7859 (ttm-80)
REVERT: A 1950 THR cc_start: 0.3471 (OUTLIER) cc_final: 0.3125 (p)
REVERT: A 2015 MET cc_start: 0.8207 (tpp) cc_final: 0.7853 (tpt)
  outliers start: 69
  outliers final: 39
  residues processed: 284
  average time/residue: 0.2971
  time to fit residues: 120.2759
Evaluate side-chains
  252 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 206
  time to evaluate  : 1.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  663 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  888 TRP
Chi-restraints excluded: chain A residue  913 LYS
Chi-restraints excluded: chain A residue  971 ARG
Chi-restraints excluded: chain A residue 1064 TRP
Chi-restraints excluded: chain A residue 1071 TYR
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1361 TRP
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1527 THR
Chi-restraints excluded: chain A residue 1532 ARG
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1537 GLU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1557 ARG
Chi-restraints excluded: chain A residue 1573 HIS
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1672 MET
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1796 LYS
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1883 TRP
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1950 THR
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 140 optimal weight:    0.9990
   chunk 115 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 169 optimal weight:    3.9990
   chunk 182 optimal weight:   10.0000
   chunk 150 optimal weight:    0.9980
   chunk 167 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
A 513 ASN
A 865 GLN
A 959 ASN
A1255 HIS
A1292 ASN
A1391 HIS
A1566 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15117  Z= 0.202
  Angle     :  0.779  11.338  20379  Z= 0.401
  Chirality :  0.046   0.224   2256
  Planarity :  0.006   0.094   2599
  Dihedral  :  8.159  60.401   2062
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 10.70 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.94 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 4.55 %
    Twisted General : 0.51 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.18), residues: 1832
  helix: -1.71 (0.18), residues: 711
  sheet: -1.37 (0.43), residues: 139
  loop : -3.38 (0.18), residues: 982

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1064 
 HIS   0.003   0.001   HIS A 734 
 PHE   0.019   0.001   PHE A 352 
 TYR   0.022   0.001   TYR A1348 
 ARG   0.005   0.000   ARG A1023 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 231
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.7474 (tt0) cc_final: 0.7098 (mt-10)
REVERT: A  189 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8805 (mm-30)
REVERT: A  237 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7669 (t0)
REVERT: A  406 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.6946 (pt)
REVERT: A  540 GLU cc_start: 0.7363 (pm20) cc_final: 0.6905 (pm20)
REVERT: A  666 THR cc_start: 0.9513 (p) cc_final: 0.9062 (t)
REVERT: A  689 LYS cc_start: 0.9048 (mttp) cc_final: 0.8820 (mttm)
REVERT: A  773 LYS cc_start: 0.9162 (tttt) cc_final: 0.8890 (ttmm)
REVERT: A  848 MET cc_start: 0.7557 (tpp) cc_final: 0.6509 (tpt)
REVERT: A  865 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8443 (mp10)
REVERT: A  874 LEU cc_start: 0.8707 (tp) cc_final: 0.8479 (tp)
REVERT: A 1079 MET cc_start: 0.7896 (mmp) cc_final: 0.6628 (mmp)
REVERT: A 1131 MET cc_start: 0.7992 (mtm) cc_final: 0.7645 (mtt)
REVERT: A 1381 GLU cc_start: 0.8694 (pm20) cc_final: 0.8189 (pm20)
REVERT: A 1463 MET cc_start: 0.3008 (ttm) cc_final: 0.1756 (tmm)
REVERT: A 1569 ASN cc_start: 0.7746 (m-40) cc_final: 0.7538 (t0)
REVERT: A 1620 GLN cc_start: 0.9533 (tp40) cc_final: 0.9269 (tp-100)
REVERT: A 1637 LEU cc_start: 0.9351 (pp) cc_final: 0.8834 (pp)
REVERT: A 1746 TRP cc_start: 0.8473 (p90) cc_final: 0.8220 (p90)
REVERT: A 2015 MET cc_start: 0.8162 (tpp) cc_final: 0.7869 (tpt)
  outliers start: 68
  outliers final: 34
  residues processed: 278
  average time/residue: 0.2744
  time to fit residues: 111.6144
Evaluate side-chains
  233 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  663 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  847 SER
Chi-restraints excluded: chain A residue  865 GLN
Chi-restraints excluded: chain A residue 1064 TRP
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1255 HIS
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1396 THR
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1433 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1573 HIS
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 167 optimal weight:    6.9990
   chunk 127 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 169 optimal weight:    6.9990
   chunk 179 optimal weight:    9.9990
   chunk 88 optimal weight:    0.0040
   chunk 160 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 237 ASN
A 865 GLN
A1151 ASN
A1255 HIS
A1292 ASN
A1403 HIS
A1566 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  15117  Z= 0.305
  Angle     :  0.785   9.839  20379  Z= 0.403
  Chirality :  0.047   0.243   2256
  Planarity :  0.005   0.098   2599
  Dihedral  :  7.306  60.310   2032
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.95 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.49 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 4.55 %
    Twisted General : 0.45 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.18), residues: 1832
  helix: -1.49 (0.18), residues: 716
  sheet: -1.46 (0.39), residues: 172
  loop : -3.25 (0.18), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1064 
 HIS   0.023   0.001   HIS A1255 
 PHE   0.022   0.002   PHE A1561 
 TYR   0.016   0.001   TYR A1071 
 ARG   0.007   0.000   ARG A1800 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 196
  time to evaluate  : 1.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.7522 (tt0) cc_final: 0.7161 (mt-10)
REVERT: A  155 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8374 (mtp85)
REVERT: A  189 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8825 (mt-10)
REVERT: A  193 TYR cc_start: 0.8310 (t80) cc_final: 0.8069 (t80)
REVERT: A  237 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7562 (t0)
REVERT: A  664 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8997 (p)
REVERT: A  689 LYS cc_start: 0.9109 (mttp) cc_final: 0.8872 (mttm)
REVERT: A  773 LYS cc_start: 0.9129 (tttt) cc_final: 0.8909 (ttmm)
REVERT: A  848 MET cc_start: 0.7756 (tpp) cc_final: 0.6740 (tpt)
REVERT: A 1027 MET cc_start: 0.8466 (ttp) cc_final: 0.8206 (mtp)
REVERT: A 1111 MET cc_start: 0.8816 (mpp) cc_final: 0.8211 (ppp)
REVERT: A 1131 MET cc_start: 0.8057 (mtm) cc_final: 0.7608 (mtp)
REVERT: A 1381 GLU cc_start: 0.8686 (pm20) cc_final: 0.8223 (pm20)
REVERT: A 1463 MET cc_start: 0.2467 (ttm) cc_final: 0.1719 (tmm)
REVERT: A 1477 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4597 (tp)
REVERT: A 1532 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8305 (mmm-85)
REVERT: A 1746 TRP cc_start: 0.8426 (p90) cc_final: 0.7826 (p90)
REVERT: A 1950 THR cc_start: 0.2918 (OUTLIER) cc_final: 0.2558 (p)
REVERT: A 2015 MET cc_start: 0.8151 (tpp) cc_final: 0.7865 (tpt)
  outliers start: 77
  outliers final: 56
  residues processed: 251
  average time/residue: 0.2690
  time to fit residues: 99.0558
Evaluate side-chains
  247 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 185
  time to evaluate  : 1.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  663 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  847 SER
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1064 TRP
Chi-restraints excluded: chain A residue 1076 THR
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1191 LEU
Chi-restraints excluded: chain A residue 1255 HIS
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1396 THR
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1474 VAL
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1532 ARG
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1557 ARG
Chi-restraints excluded: chain A residue 1566 GLN
Chi-restraints excluded: chain A residue 1573 HIS
Chi-restraints excluded: chain A residue 1574 VAL
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1672 MET
Chi-restraints excluded: chain A residue 1709 THR
Chi-restraints excluded: chain A residue 1739 ASP
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1950 THR
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 149 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 133 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 153 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 161 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 748 ASN
A 799 HIS
A 959 ASN
A1255 HIS
A1292 ASN
A1566 GLN
** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15117  Z= 0.235
  Angle     :  0.756  10.679  20379  Z= 0.383
  Chirality :  0.046   0.234   2256
  Planarity :  0.005   0.098   2599
  Dihedral  :  7.085  60.713   2032
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.19 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 21.77 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.56 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.19), residues: 1832
  helix: -1.28 (0.19), residues: 721
  sheet: -1.33 (0.41), residues: 164
  loop : -3.08 (0.19), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1064 
 HIS   0.009   0.001   HIS A1255 
 PHE   0.020   0.001   PHE A 352 
 TYR   0.015   0.001   TYR A1071 
 ARG   0.007   0.000   ARG A1189 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 204
  time to evaluate  : 1.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8785 (mt-10)
REVERT: A  193 TYR cc_start: 0.8324 (t80) cc_final: 0.8084 (t80)
REVERT: A  406 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7211 (pt)
REVERT: A  411 PHE cc_start: 0.6797 (m-10) cc_final: 0.6551 (m-10)
REVERT: A  625 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: A  664 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.9010 (p)
REVERT: A  666 THR cc_start: 0.9499 (p) cc_final: 0.9124 (t)
REVERT: A  689 LYS cc_start: 0.9113 (mttp) cc_final: 0.8876 (mttm)
REVERT: A  773 LYS cc_start: 0.9160 (tttt) cc_final: 0.8900 (ttmm)
REVERT: A  848 MET cc_start: 0.7617 (tpp) cc_final: 0.7262 (tpt)
REVERT: A 1027 MET cc_start: 0.8448 (ttp) cc_final: 0.8080 (mtp)
REVERT: A 1079 MET cc_start: 0.7916 (mmp) cc_final: 0.7658 (mmp)
REVERT: A 1381 GLU cc_start: 0.8679 (pm20) cc_final: 0.8222 (pm20)
REVERT: A 1463 MET cc_start: 0.2522 (ttm) cc_final: 0.1747 (tmm)
REVERT: A 1477 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4477 (tp)
REVERT: A 1554 GLU cc_start: 0.6332 (tp30) cc_final: 0.6019 (tp30)
REVERT: A 1635 MET cc_start: 0.8263 (ppp) cc_final: 0.7563 (ppp)
REVERT: A 1746 TRP cc_start: 0.8427 (p90) cc_final: 0.7823 (p90)
REVERT: A 1832 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8074 (mm)
REVERT: A 2015 MET cc_start: 0.8153 (tpp) cc_final: 0.7897 (tpt)
  outliers start: 74
  outliers final: 50
  residues processed: 258
  average time/residue: 0.2727
  time to fit residues: 104.3958
Evaluate side-chains
  239 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 185
  time to evaluate  : 1.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  799 HIS
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1173 VAL
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1255 HIS
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1396 THR
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1474 VAL
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1573 HIS
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1739 ASP
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1832 ILE
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1883 TRP
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1955 ASP
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1969 VAL
Chi-restraints excluded: chain A residue 1977 ASP
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 161 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0060
   chunk 105 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 179 optimal weight:    9.9990
   chunk 149 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0970
   chunk 59 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.8200

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

Flipped N/Q/H residues before XYZ refinement:
A 959 ASN
A1255 HIS
A1292 ASN
** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15117  Z= 0.226
  Angle     :  0.742  10.063  20379  Z= 0.375
  Chirality :  0.045   0.227   2256
  Planarity :  0.005   0.098   2599
  Dihedral  :  6.756  60.466   2030
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.74 %
    Favored  : 87.94 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 23.36 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.45 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.19), residues: 1832
  helix: -1.08 (0.19), residues: 727
  sheet: -1.18 (0.41), residues: 164
  loop : -3.05 (0.19), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A1064 
 HIS   0.014   0.001   HIS A1255 
 PHE   0.019   0.001   PHE A 352 
 TYR   0.013   0.001   TYR A1864 
 ARG   0.013   0.000   ARG A1829 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 199
  time to evaluate  : 1.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8756 (mt-10)
REVERT: A  193 TYR cc_start: 0.8343 (t80) cc_final: 0.8069 (t80)
REVERT: A  405 LYS cc_start: 0.7268 (pttt) cc_final: 0.7016 (pttm)
REVERT: A  406 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7103 (pt)
REVERT: A  411 PHE cc_start: 0.6685 (m-10) cc_final: 0.6459 (m-10)
REVERT: A  625 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: A  666 THR cc_start: 0.9503 (p) cc_final: 0.9170 (t)
REVERT: A  689 LYS cc_start: 0.9108 (mttp) cc_final: 0.8861 (mttm)
REVERT: A  773 LYS cc_start: 0.9160 (tttt) cc_final: 0.8920 (ttmm)
REVERT: A  848 MET cc_start: 0.7544 (tpp) cc_final: 0.7174 (tpt)
REVERT: A 1079 MET cc_start: 0.8113 (mmp) cc_final: 0.7856 (mmp)
REVERT: A 1111 MET cc_start: 0.8856 (mpp) cc_final: 0.8176 (ppp)
REVERT: A 1381 GLU cc_start: 0.8649 (pm20) cc_final: 0.8182 (pm20)
REVERT: A 1463 MET cc_start: 0.2594 (ttm) cc_final: 0.1804 (tmm)
REVERT: A 1635 MET cc_start: 0.8331 (ppp) cc_final: 0.7836 (ppp)
REVERT: A 1641 TYR cc_start: 0.8877 (m-80) cc_final: 0.8673 (m-80)
REVERT: A 1746 TRP cc_start: 0.8402 (p90) cc_final: 0.7807 (p90)
REVERT: A 2015 MET cc_start: 0.8198 (tpp) cc_final: 0.7941 (tpt)
  outliers start: 71
  outliers final: 51
  residues processed: 252
  average time/residue: 0.2596
  time to fit residues: 97.9376
Evaluate side-chains
  239 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 187
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  322 GLN
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  810 CYS
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  954 ASN
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1173 VAL
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1255 HIS
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1474 VAL
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1739 ASP
Chi-restraints excluded: chain A residue 1743 THR
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1969 VAL
Chi-restraints excluded: chain A residue 1977 ASP
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 173 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 131 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 179 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 799 HIS
** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 ASN
** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15117  Z= 0.248
  Angle     :  0.749   9.994  20379  Z= 0.379
  Chirality :  0.045   0.238   2256
  Planarity :  0.005   0.099   2599
  Dihedral  :  6.641  60.821   2028
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.14 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 23.91 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.19), residues: 1832
  helix: -0.89 (0.19), residues: 713
  sheet: -1.19 (0.41), residues: 164
  loop : -2.93 (0.19), residues: 955

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1989 
 HIS   0.015   0.001   HIS A1255 
 PHE   0.023   0.001   PHE A 166 
 TYR   0.013   0.001   TYR A1071 
 ARG   0.004   0.000   ARG A  30 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 201
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8741 (mt-10)
REVERT: A  193 TYR cc_start: 0.8385 (t80) cc_final: 0.8124 (t80)
REVERT: A  252 MET cc_start: 0.8251 (mmm) cc_final: 0.7932 (mmt)
REVERT: A  405 LYS cc_start: 0.7243 (pttt) cc_final: 0.7017 (pttm)
REVERT: A  406 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7079 (pt)
REVERT: A  411 PHE cc_start: 0.6740 (m-10) cc_final: 0.6537 (m-10)
REVERT: A  625 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: A  666 THR cc_start: 0.9454 (p) cc_final: 0.9108 (t)
REVERT: A  686 MET cc_start: 0.8699 (mmm) cc_final: 0.8465 (tpp)
REVERT: A  773 LYS cc_start: 0.9164 (tttt) cc_final: 0.8867 (ttmm)
REVERT: A  778 GLU cc_start: 0.8027 (tp30) cc_final: 0.7803 (tp30)
REVERT: A  848 MET cc_start: 0.7666 (tpp) cc_final: 0.6972 (tpt)
REVERT: A  878 MET cc_start: 0.8828 (ptp) cc_final: 0.8614 (mtm)
REVERT: A  887 MET cc_start: 0.7752 (tpp) cc_final: 0.6893 (tpp)
REVERT: A  925 MET cc_start: 0.8107 (mmm) cc_final: 0.7893 (mmm)
REVERT: A 1079 MET cc_start: 0.8208 (mmp) cc_final: 0.7945 (mmp)
REVERT: A 1111 MET cc_start: 0.8794 (mpp) cc_final: 0.8157 (ppp)
REVERT: A 1140 MET cc_start: 0.8465 (ttp) cc_final: 0.8175 (tmm)
REVERT: A 1381 GLU cc_start: 0.8619 (pm20) cc_final: 0.8175 (pm20)
REVERT: A 1463 MET cc_start: 0.2540 (ttm) cc_final: 0.1742 (tmm)
REVERT: A 1477 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4586 (tp)
REVERT: A 1635 MET cc_start: 0.8390 (ppp) cc_final: 0.7772 (ppp)
REVERT: A 1746 TRP cc_start: 0.8386 (p90) cc_final: 0.7788 (p90)
REVERT: A 1826 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7234 (mmp)
REVERT: A 2015 MET cc_start: 0.8185 (tpp) cc_final: 0.7937 (tpt)
  outliers start: 68
  outliers final: 58
  residues processed: 248
  average time/residue: 0.2692
  time to fit residues: 98.6234
Evaluate side-chains
  249 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 188
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  799 HIS
Chi-restraints excluded: chain A residue  810 CYS
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  954 ASN
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1173 VAL
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1255 HIS
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1372 LEU
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1444 MET
Chi-restraints excluded: chain A residue 1474 VAL
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1573 HIS
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1709 THR
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1739 ASP
Chi-restraints excluded: chain A residue 1743 THR
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1826 MET
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1969 VAL
Chi-restraints excluded: chain A residue 1977 ASP
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 107 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0010
   chunk 34 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 88 optimal weight:    0.0030
   chunk 16 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
A 322 GLN
A 748 ASN
A 959 ASN
A1151 ASN
A1245 HIS
A1255 HIS
A1292 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15117  Z= 0.183
  Angle     :  0.729  10.512  20379  Z= 0.366
  Chirality :  0.044   0.221   2256
  Planarity :  0.005   0.095   2599
  Dihedral  :  6.413  59.860   2028
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.26 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.89 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.19), residues: 1832
  helix: -0.75 (0.19), residues: 723
  sheet: -0.72 (0.43), residues: 150
  loop : -2.93 (0.19), residues: 959

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 520 
 HIS   0.013   0.001   HIS A 799 
 PHE   0.020   0.001   PHE A 166 
 TYR   0.014   0.001   TYR A1864 
 ARG   0.008   0.000   ARG A 832 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 205
  time to evaluate  : 1.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: A  193 TYR cc_start: 0.8296 (t80) cc_final: 0.8094 (t80)
REVERT: A  252 MET cc_start: 0.8179 (mmm) cc_final: 0.7875 (mmp)
REVERT: A  405 LYS cc_start: 0.7428 (pttt) cc_final: 0.7165 (pttm)
REVERT: A  406 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6949 (pt)
REVERT: A  625 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: A  626 LYS cc_start: 0.9025 (tppt) cc_final: 0.8774 (tppt)
REVERT: A  773 LYS cc_start: 0.9127 (tttt) cc_final: 0.8795 (ttmm)
REVERT: A  848 MET cc_start: 0.7530 (tpp) cc_final: 0.7096 (tpt)
REVERT: A  950 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7139 (mm-30)
REVERT: A 1111 MET cc_start: 0.8716 (mpp) cc_final: 0.8127 (ppp)
REVERT: A 1140 MET cc_start: 0.8396 (ttp) cc_final: 0.8060 (tmm)
REVERT: A 1324 ARG cc_start: 0.7802 (ttt90) cc_final: 0.7563 (ttt90)
REVERT: A 1381 GLU cc_start: 0.8638 (pm20) cc_final: 0.8190 (pm20)
REVERT: A 1463 MET cc_start: 0.2907 (ttm) cc_final: 0.2213 (tmm)
REVERT: A 1635 MET cc_start: 0.8251 (ppp) cc_final: 0.7835 (ppp)
REVERT: A 1826 MET cc_start: 0.7645 (mmt) cc_final: 0.7429 (mmp)
REVERT: A 2015 MET cc_start: 0.8110 (tpp) cc_final: 0.7866 (tpt)
  outliers start: 51
  outliers final: 38
  residues processed: 241
  average time/residue: 0.2731
  time to fit residues: 98.5061
Evaluate side-chains
  229 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 190
  time to evaluate  : 1.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1173 VAL
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1709 THR
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1743 THR
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1955 ASP
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1977 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 163 optimal weight:    6.9990
   chunk 171 optimal weight:    5.9990
   chunk 156 optimal weight:    7.9990
   chunk 167 optimal weight:    6.9990
   chunk 100 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 131 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 150 optimal weight:    0.0060
   chunk 158 optimal weight:    8.9990
   chunk 166 optimal weight:   30.0000
   overall best weight:    5.0004

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

Flipped N/Q/H residues before XYZ refinement:
A 376 ASN
** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 ASN
A 959 ASN
A1011 HIS
A1292 ASN
** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  15117  Z= 0.456
  Angle     :  0.859  10.966  20379  Z= 0.438
  Chirality :  0.050   0.264   2256
  Planarity :  0.006   0.103   2599
  Dihedral  :  6.724  62.021   2026
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 12.77 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.77 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 4.55 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.19), residues: 1832
  helix: -0.86 (0.19), residues: 719
  sheet: -0.93 (0.42), residues: 153
  loop : -2.92 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.003   TRP A1746 
 HIS   0.005   0.001   HIS A1564 
 PHE   0.021   0.002   PHE A 166 
 TYR   0.021   0.002   TYR A1348 
 ARG   0.006   0.001   ARG A1928 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 182
  time to evaluate  : 1.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.8424 (t80) cc_final: 0.8159 (t80)
REVERT: A  208 MET cc_start: 0.3641 (pmm) cc_final: 0.3357 (pmm)
REVERT: A  625 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8489 (tm-30)
REVERT: A  626 LYS cc_start: 0.9114 (tppt) cc_final: 0.8910 (tppt)
REVERT: A  773 LYS cc_start: 0.9156 (tttt) cc_final: 0.8873 (ttmm)
REVERT: A  778 GLU cc_start: 0.8168 (tp30) cc_final: 0.7871 (tp30)
REVERT: A  925 MET cc_start: 0.8190 (mmm) cc_final: 0.7980 (mmm)
REVERT: A 1140 MET cc_start: 0.8581 (ttp) cc_final: 0.8286 (tmm)
REVERT: A 1381 GLU cc_start: 0.8640 (pm20) cc_final: 0.8164 (pm20)
REVERT: A 1416 LEU cc_start: 0.9171 (tp) cc_final: 0.8894 (tp)
REVERT: A 1463 MET cc_start: 0.2382 (ttm) cc_final: 0.1525 (tmm)
REVERT: A 1477 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.4572 (tp)
REVERT: A 1635 MET cc_start: 0.8401 (ppp) cc_final: 0.8193 (ppp)
REVERT: A 2015 MET cc_start: 0.8184 (tpp) cc_final: 0.7951 (tpt)
  outliers start: 63
  outliers final: 47
  residues processed: 227
  average time/residue: 0.2797
  time to fit residues: 94.4551
Evaluate side-chains
  219 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 171
  time to evaluate  : 1.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  810 CYS
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  866 THR
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1372 LEU
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1444 MET
Chi-restraints excluded: chain A residue 1447 ILE
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1709 THR
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1835 LEU
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1977 ASP
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 176 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 185 optimal weight:    2.9990
   chunk 170 optimal weight:    5.9990
   chunk 147 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 113 optimal weight:    0.1980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 ASN
A1255 HIS
A1638 ASN
** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15117  Z= 0.224
  Angle     :  0.778  10.602  20379  Z= 0.393
  Chirality :  0.046   0.229   2256
  Planarity :  0.005   0.097   2599
  Dihedral  :  6.569  61.205   2026
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.26 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 26.24 %
    Favored  : 70.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.45 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.19), residues: 1832
  helix: -0.63 (0.19), residues: 726
  sheet: -0.62 (0.43), residues: 140
  loop : -2.92 (0.19), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.002   TRP A1746 
 HIS   0.004   0.001   HIS A1564 
 PHE   0.018   0.001   PHE A 166 
 TYR   0.020   0.001   TYR A1864 
 ARG   0.005   0.000   ARG A1800 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 192
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8661 (mm-30)
REVERT: A  193 TYR cc_start: 0.8292 (t80) cc_final: 0.8073 (t80)
REVERT: A  625 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8432 (tm-30)
REVERT: A  626 LYS cc_start: 0.9083 (tppt) cc_final: 0.8883 (tppt)
REVERT: A  713 ILE cc_start: 0.9041 (mt) cc_final: 0.8834 (mt)
REVERT: A  773 LYS cc_start: 0.9125 (tttt) cc_final: 0.8809 (ttmm)
REVERT: A  778 GLU cc_start: 0.8018 (tp30) cc_final: 0.7786 (tp30)
REVERT: A  925 MET cc_start: 0.8179 (mmm) cc_final: 0.7922 (mmm)
REVERT: A 1027 MET cc_start: 0.8391 (mmm) cc_final: 0.8097 (mmm)
REVERT: A 1111 MET cc_start: 0.8747 (mpp) cc_final: 0.8213 (ppp)
REVERT: A 1140 MET cc_start: 0.8465 (ttp) cc_final: 0.8212 (tmm)
REVERT: A 1381 GLU cc_start: 0.8626 (pm20) cc_final: 0.8182 (pm20)
REVERT: A 1463 MET cc_start: 0.2485 (ttm) cc_final: 0.1382 (tmm)
REVERT: A 1477 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4358 (tp)
REVERT: A 1638 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8485 (t0)
REVERT: A 1689 LEU cc_start: 0.6530 (pt) cc_final: 0.6286 (pp)
  outliers start: 49
  outliers final: 38
  residues processed: 227
  average time/residue: 0.2649
  time to fit residues: 89.2433
Evaluate side-chains
  224 residues out of total 1635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  408 TYR
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 GLN
Chi-restraints excluded: chain A residue  724 GLU
Chi-restraints excluded: chain A residue  810 CYS
Chi-restraints excluded: chain A residue  837 ILE
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1516 LEU
Chi-restraints excluded: chain A residue 1541 LEU
Chi-restraints excluded: chain A residue 1595 THR
Chi-restraints excluded: chain A residue 1638 ASN
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1709 THR
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1769 CYS
Chi-restraints excluded: chain A residue 1806 VAL
Chi-restraints excluded: chain A residue 1811 ARG
Chi-restraints excluded: chain A residue 1835 LEU
Chi-restraints excluded: chain A residue 1868 ASN
Chi-restraints excluded: chain A residue 1886 LEU
Chi-restraints excluded: chain A residue 1910 ILE
Chi-restraints excluded: chain A residue 1954 VAL
Chi-restraints excluded: chain A residue 1957 LEU
Chi-restraints excluded: chain A residue 1977 ASP
Chi-restraints excluded: chain A residue 2007 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 157 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 136 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 147 optimal weight:    0.0770
   chunk 61 optimal weight:    0.8980
   chunk 151 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.9340

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

Flipped N/Q/H residues before XYZ refinement:
A 959 ASN
** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1292 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.109474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.083519 restraints weight = 36134.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 4.25
r_work: 0.3143 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15117  Z= 0.198
  Angle     :  0.777  13.449  20379  Z= 0.389
  Chirality :  0.045   0.231   2256
  Planarity :  0.005   0.096   2599
  Dihedral  :  6.453  60.046   2026
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 10.75 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 26.67 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.51 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.19), residues: 1832
  helix: -0.54 (0.20), residues: 730
  sheet: -0.55 (0.43), residues: 140
  loop : -2.89 (0.19), residues: 962

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A1746 
 HIS   0.003   0.000   HIS A 103 
 PHE   0.018   0.001   PHE A 166 
 TYR   0.019   0.001   TYR A1641 
 ARG   0.005   0.000   ARG A  30 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3212.34 seconds
wall clock time: 58 minutes 9.55 seconds (3489.55 seconds total)