Starting phenix.real_space_refine
on Tue Nov 19 23:43:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8g_16475/11_2024/8c8g_16475.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.040
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: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C   12995      2.51       5
     N    3303      2.21       5
     O    4013      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 20362
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1335, 10790
          Classifications: {'peptide': 1335}
          Link IDs: {'PTRANS': 37, 'TRANS': 1297}
    Chain: "B"
      Number of atoms: 9572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1195, 9572
          Classifications: {'peptide': 1195}
          Link IDs: {'PTRANS': 39, 'TRANS': 1155}
  Time building chain proxies: 11.96, per 1000 atoms: 0.59
  Number of scatterers: 20362
  At special positions: 0
  Unit cell: (127.92, 116.44, 151.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    4013      8.00
     N    3303      7.00
     C   12995      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 366 " distance=2.07

  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: 4.83
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4806

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 36 sheets defined
      26.3% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 100 through 122
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.813A  pdb=" N   PHE A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 261
      removed outlier: 3.907A  pdb=" N   LEU A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   HIS A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 275
      No H-bonds generated for 'chain 'A' and resid 273 through 275'
    Processing helix  chain 'A' and resid 294 through 300
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 331 through 335
      removed outlier: 3.590A  pdb=" N   SER A 335 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 356 through 367
    Processing helix  chain 'A' and resid 373 through 376
      removed outlier: 3.975A  pdb=" N   LYS A 376 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 373 through 376'
    Processing helix  chain 'A' and resid 385 through 391
    Processing helix  chain 'A' and resid 392 through 394
      No H-bonds generated for 'chain 'A' and resid 392 through 394'
    Processing helix  chain 'A' and resid 396 through 404
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.531A  pdb=" N   THR A 413 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 414 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 414'
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 566 through 574
    Processing helix  chain 'A' and resid 591 through 596
      removed outlier: 3.656A  pdb=" N   PHE A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 3.574A  pdb=" N   GLU A 615 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 639
    Processing helix  chain 'A' and resid 659 through 666
    Processing helix  chain 'A' and resid 671 through 676
    Processing helix  chain 'A' and resid 716 through 750
      removed outlier: 4.019A  pdb=" N   VAL A 728 " --> pdb=" O   PHE A 724 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 740 " --> pdb=" O   LYS A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 781
      removed outlier: 3.525A  pdb=" N   THR A 774 " --> pdb=" O   LYS A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 801
    Processing helix  chain 'A' and resid 803 through 830
    Processing helix  chain 'A' and resid 830 through 861
      removed outlier: 3.565A  pdb=" N   GLN A 841 " --> pdb=" O   GLU A 837 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLU A 855 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU A 856 " --> pdb=" O   ASP A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 879
    Processing helix  chain 'A' and resid 883 through 905
      removed outlier: 3.510A  pdb=" N   VAL A 896 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A 897 " --> pdb=" O   HIS A 893 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 902 " --> pdb=" O   LYS A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1121 through 1133
      removed outlier: 3.865A  pdb=" N   HIS A1133 " --> pdb=" O   PHE A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1285 through 1290
    Processing helix  chain 'B' and resid 69 through 88
      removed outlier: 3.537A  pdb=" N   LEU B  76 " --> pdb=" O   GLN B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 101
    Processing helix  chain 'B' and resid 152 through 156
      removed outlier: 3.530A  pdb=" N   SER B 155 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 199
      removed outlier: 3.531A  pdb=" N   GLY B 189 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS B 193 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE B 196 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG B 197 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 229
    Processing helix  chain 'B' and resid 248 through 260
      removed outlier: 3.569A  pdb=" N   ALA B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 280
      removed outlier: 3.647A  pdb=" N   TYR B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 289
    Processing helix  chain 'B' and resid 309 through 315
    Processing helix  chain 'B' and resid 391 through 397
      removed outlier: 3.642A  pdb=" N   THR B 396 " --> pdb=" O   SER B 392 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.558A  pdb=" N   ALA B 440 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
      removed outlier: 3.815A  pdb=" N   ILE B 450 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 463
      removed outlier: 4.522A  pdb=" N   ASP B 461 " --> pdb=" O   SER B 457 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASP B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 479
    Processing helix  chain 'B' and resid 484 through 500
      removed outlier: 4.075A  pdb=" N   PHE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 528
    Processing helix  chain 'B' and resid 539 through 544
    Processing helix  chain 'B' and resid 559 through 561
      No H-bonds generated for 'chain 'B' and resid 559 through 561'
    Processing helix  chain 'B' and resid 562 through 575
      removed outlier: 4.264A  pdb=" N   TYR B 566 " --> pdb=" O   GLN B 562 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU B 567 " --> pdb=" O   LEU B 563 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE B 568 " --> pdb=" O   LYS B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 603
      removed outlier: 3.809A  pdb=" N   LEU B 582 " --> pdb=" O   ARG B 578 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU B 585 " --> pdb=" O   ARG B 581 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B 603 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 650
      removed outlier: 3.531A  pdb=" N   TYR B 626 " --> pdb=" O   TYR B 622 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 632 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR B 645 " --> pdb=" O   LYS B 641 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE B 648 " --> pdb=" O   VAL B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 662
    Processing helix  chain 'B' and resid 665 through 674
      removed outlier: 3.653A  pdb=" N   LEU B 671 " --> pdb=" O   ASP B 667 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 41
      removed outlier: 6.896A  pdb=" N   ILE A  63 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL A 186 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 41
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 167
      removed outlier: 3.926A  pdb=" N   GLY A 179 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU A 166 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   LYS A 177 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 241
      removed outlier: 3.511A  pdb=" N   THR A 451 " --> pdb=" O   ARG A 425 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 282
    Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371
      removed outlier: 3.520A  pdb=" N   LYS A 370 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 477
      removed outlier: 7.734A  pdb=" N   VAL A 560 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   GLU A 464 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 562 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLU A 466 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 589
    Processing sheet with id=AB1, first strand: chain 'A' and resid 644 through 645
    Processing sheet with id=AB2, first strand: chain 'A' and resid 923 through 924
    Processing sheet with id=AB3, first strand: chain 'A' and resid 941 through 944
      removed outlier: 3.967A  pdb=" N   VAL A 976 " --> pdb=" O   PHE A1099 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   ILE A1011 " --> pdb=" O   TYR A1102 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU A1029 " --> pdb=" O   ILE A1011 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   SER A1013 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   LEU A1027 " --> pdb=" O   SER A1013 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   SER A1015 " --> pdb=" O   GLU A1025 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   GLU A1025 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL A1017 " --> pdb=" O   GLU A1023 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   GLU A1023 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE A1036 " --> pdb=" O   ILE A1051 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 952 through 953
      removed outlier: 10.918A  pdb=" N   GLN A 958 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   ASP A1112 " --> pdb=" O   GLN A 958 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   LEU A1110 " --> pdb=" O   ARG A 999 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ARG A 999 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ASP A1112 " --> pdb=" O   TRP A 997 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   TRP A 997 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ILE A1072 " --> pdb=" O   LEU A1083 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU A1083 " --> pdb=" O   ILE A1072 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1081 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1220 through 1223
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1160 through 1161
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1179 through 1180
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1229 through 1235
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1259 through 1261
      removed outlier: 5.194A  pdb=" N   LEU A1273 " --> pdb=" O   ILE A1297 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1278 through 1279
    Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 130
      removed outlier: 3.991A  pdb=" N   HIS B 127 " --> pdb=" O   CYS B 118 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLN B 117 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ASN B   9 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LEU B  23 " --> pdb=" O   TYR B  12 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 181
      removed outlier: 3.569A  pdb=" N   ARG B 179 " --> pdb=" O   ASN B 174 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 212
      removed outlier: 6.539A  pdb=" N   TYR B 219 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 340 through 341
      removed outlier: 6.263A  pdb=" N   LYS B 340 " --> pdb=" O   THR B 429 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AC7, first strand: chain 'B' and resid 502 through 503
    Processing sheet with id=AC8, first strand: chain 'B' and resid 690 through 694
      removed outlier: 7.638A  pdb=" N   SER B 711 " --> pdb=" O   PRO B 700 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU B 702 " --> pdb=" O   ILE B 709 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASP B 707 " --> pdb=" O   LEU B 704 " (cutoff:3.500A)
      removed outlier: 9.774A  pdb=" N   GLU B 708 " --> pdb=" O   ASN B 739 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   ASN B 739 " --> pdb=" O   GLU B 708 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE B 736 " --> pdb=" O   LEU B 841 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 718
      removed outlier: 6.592A  pdb=" N   LEU B 850 " --> pdb=" O   LYS B 756 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LYS B 756 " --> pdb=" O   LEU B 850 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER B 852 " --> pdb=" O   THR B 754 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   ASP B 815 " --> pdb=" O   LEU B 821 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   LEU B 821 " --> pdb=" O   ASP B 815 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 943 through 947
      removed outlier: 7.989A  pdb=" N   LEU B 928 " --> pdb=" O   GLU B 888 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   GLU B 888 " --> pdb=" O   LEU B 928 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 902 through 905
      removed outlier: 4.381A  pdb=" N   LEU B1011 " --> pdb=" O   PRO B 912 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 955 through 959
      removed outlier: 3.523A  pdb=" N   TYR B 955 " --> pdb=" O   VAL B 966 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 988 through 992
    Processing sheet with id=AD5, first strand: chain 'B' and resid 1047 through 1050
    Processing sheet with id=AD6, first strand: chain 'B' and resid 1055 through 1056
      removed outlier: 6.515A  pdb=" N   LEU B1055 " --> pdb=" O   LYS B1121 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'B' and resid 1085 through 1088
    Processing sheet with id=AD8, first strand: chain 'B' and resid 1126 through 1128
      removed outlier: 3.979A  pdb=" N   SER B1126 " --> pdb=" O   ILE B1150 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1133
      removed outlier: 6.995A  pdb=" N   SER B1132 " --> pdb=" O   THR B1198 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR B1184 " --> pdb=" O   ILE B1191 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B1193 " --> pdb=" O   PHE B1182 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B1181 " --> pdb=" O   GLU B1167 " (cutoff:3.500A)

    704 hydrogen bonds defined for protein.
    1947 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: 8.94

  Time building geometry restraints manager: 5.60 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 3527
        1.31 -     1.44: 5482
        1.44 -     1.57: 11675
        1.57 -     1.71: 0
        1.71 -     1.84: 93
  Bond restraints: 20777
  Sorted by residual:
  bond pdb=" C   PRO B 209 "
       pdb=" O   PRO B 209 "
    ideal  model  delta    sigma   weight residual
    1.233  1.172  0.061 1.16e-02 7.43e+03 2.76e+01
  bond pdb=" C   PRO A1329 "
       pdb=" O   PRO A1329 "
    ideal  model  delta    sigma   weight residual
    1.233  1.179  0.054 1.12e-02 7.97e+03 2.32e+01
  bond pdb=" CA  SER B 233 "
       pdb=" CB  SER B 233 "
    ideal  model  delta    sigma   weight residual
    1.527  1.460  0.067 1.44e-02 4.82e+03 2.16e+01
  bond pdb=" CA  SER B1020 "
       pdb=" CB  SER B1020 "
    ideal  model  delta    sigma   weight residual
    1.530  1.463  0.067 1.55e-02 4.16e+03 1.86e+01
  bond pdb=" CA  SER A1230 "
       pdb=" CB  SER A1230 "
    ideal  model  delta    sigma   weight residual
    1.536  1.451  0.085 2.08e-02 2.31e+03 1.66e+01
  ... (remaining 20772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 23489
        2.06 -     4.12: 4384
        4.12 -     6.18: 245
        6.18 -     8.24: 18
        8.24 -    10.30: 3
  Bond angle restraints: 28139
  Sorted by residual:
  angle pdb=" N   PRO B 241 "
        pdb=" CA  PRO B 241 "
        pdb=" CB  PRO B 241 "
      ideal   model   delta    sigma   weight residual
     103.25   92.95   10.30 1.05e+00 9.07e-01 9.62e+01
  angle pdb=" N   ARG A1301 "
        pdb=" CA  ARG A1301 "
        pdb=" C   ARG A1301 "
      ideal   model   delta    sigma   weight residual
     110.53  102.99    7.54 1.29e+00 6.01e-01 3.42e+01
  angle pdb=" N   ARG A1301 "
        pdb=" CA  ARG A1301 "
        pdb=" CB  ARG A1301 "
      ideal   model   delta    sigma   weight residual
     110.44  118.78   -8.34 1.43e+00 4.89e-01 3.40e+01
  angle pdb=" N   GLN B 281 "
        pdb=" CA  GLN B 281 "
        pdb=" C   GLN B 281 "
      ideal   model   delta    sigma   weight residual
     114.31  107.26    7.05 1.29e+00 6.01e-01 2.99e+01
  angle pdb=" N   VAL A  84 "
        pdb=" CA  VAL A  84 "
        pdb=" C   VAL A  84 "
      ideal   model   delta    sigma   weight residual
     113.71  108.63    5.08 9.50e-01 1.11e+00 2.86e+01
  ... (remaining 28134 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 11218
       17.88 -    35.76: 1077
       35.76 -    53.63: 160
       53.63 -    71.51: 31
       71.51 -    89.39: 11
  Dihedral angle restraints: 12497
    sinusoidal: 5033
      harmonic: 7464
  Sorted by residual:
  dihedral pdb=" CA  ASN B 846 "
           pdb=" C   ASN B 846 "
           pdb=" N   GLU B 847 "
           pdb=" CA  GLU B 847 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.18  -29.82     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  LYS A 964 "
           pdb=" C   LYS A 964 "
           pdb=" N   ASP A 965 "
           pdb=" CA  ASP A 965 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.99   28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  PRO B 686 "
           pdb=" C   PRO B 686 "
           pdb=" N   SER B 687 "
           pdb=" CA  SER B 687 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.12  -27.88     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 12494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1574
       0.060 -    0.120: 1095
       0.120 -    0.181: 409
       0.181 -    0.241: 54
       0.241 -    0.301: 9
  Chirality restraints: 3141
  Sorted by residual:
  chirality pdb=" CA  VAL B 823 "
            pdb=" N   VAL B 823 "
            pdb=" C   VAL B 823 "
            pdb=" CB  VAL B 823 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  ILE B 896 "
            pdb=" N   ILE B 896 "
            pdb=" C   ILE B 896 "
            pdb=" CB  ILE B 896 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  PHE B 244 "
            pdb=" N   PHE B 244 "
            pdb=" C   PHE B 244 "
            pdb=" CB  PHE B 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 3138 not shown)

  Planarity restraints: 3624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1099 "   -0.043 2.00e-02 2.50e+03   2.97e-02 1.54e+01
        pdb=" CG  PHE A1099 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1099 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1099 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1099 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1099 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1099 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 989 "   -0.047 2.00e-02 2.50e+03   2.39e-02 1.14e+01
        pdb=" CG  TYR B 989 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 989 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 989 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 989 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 989 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 989 "   -0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR B 989 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B1039 "   -0.045 2.00e-02 2.50e+03   2.38e-02 1.14e+01
        pdb=" CG  TYR B1039 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR B1039 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B1039 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR B1039 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR B1039 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B1039 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B1039 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 3621 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1767
        2.74 -     3.28: 19591
        3.28 -     3.82: 32663
        3.82 -     4.36: 46348
        4.36 -     4.90: 74298
  Nonbonded interactions: 174667
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 239 "
            pdb=" C   GLN B 240 "
     model   vdw
     2.198 3.270
  nonbonded pdb=" O   LEU B  93 "
            pdb=" OG1 THR B  97 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   LYS A 813 "
            pdb=" OG1 THR A 817 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ALA B 111 "
            pdb=" OG1 THR B 115 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OD2 ASP A 243 "
            pdb=" OG1 THR A 245 "
     model   vdw
     2.277 3.040
  ... (remaining 174662 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.390
  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:             0.020
  Extract box with map and model:          0.790
  Check model and map are aligned:         0.150
  Set scattering table:                    0.180
  Process input model:                     47.490
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
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   0.085  20777  Z= 0.828
  Angle     :  1.497  10.297  28139  Z= 1.049
  Chirality :  0.083   0.301   3141
  Planarity :  0.007   0.057   3624
  Dihedral  : 14.188  89.389   7688
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.96 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  5.92 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.13), residues: 2526
  helix: -3.95 (0.11), residues: 638
  sheet: -2.36 (0.23), residues: 444
  loop : -2.40 (0.14), residues: 1444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.009   TRP B 631 
 HIS   0.035   0.004   HIS A 922 
 PHE   0.053   0.007   PHE A1099 
 TYR   0.050   0.008   TYR A1108 
 ARG   0.018   0.002   ARG A 766 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 365
  time to evaluate  : 2.467 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASN cc_start: 0.8616 (m110) cc_final: 0.8409 (m-40)
REVERT: A   46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7793 (tt0)
REVERT: A   48 ARG cc_start: 0.6935 (ptp-110) cc_final: 0.6414 (ptp-110)
REVERT: A   94 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7758 (mtm-85)
REVERT: A  228 SER cc_start: 0.8822 (m) cc_final: 0.8556 (t)
REVERT: A  251 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8121 (mm-30)
REVERT: A  383 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7176 (ttt-90)
REVERT: A  387 ARG cc_start: 0.8569 (ttm170) cc_final: 0.8130 (mtp85)
REVERT: A  505 ASP cc_start: 0.7714 (t0) cc_final: 0.7457 (t0)
REVERT: A  530 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7172 (mtm110)
REVERT: A  554 ASP cc_start: 0.8579 (t70) cc_final: 0.8267 (t0)
REVERT: A  576 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6769 (tm)
REVERT: A  611 MET cc_start: 0.8574 (mtm) cc_final: 0.8175 (mtt)
REVERT: A  615 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7126 (mp0)
REVERT: A  645 GLU cc_start: 0.9008 (mp0) cc_final: 0.8745 (mp0)
REVERT: A  711 TYR cc_start: 0.6992 (t80) cc_final: 0.6674 (t80)
REVERT: A  834 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7868 (tttp)
REVERT: A  868 TYR cc_start: 0.8443 (t80) cc_final: 0.7833 (t80)
REVERT: A  876 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8570 (mtm110)
REVERT: A  971 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8087 (ttpp)
REVERT: A 1209 MET cc_start: 0.6007 (ptt) cc_final: 0.4620 (tmm)
REVERT: B   11 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7862 (ttp-170)
REVERT: B  107 LYS cc_start: 0.8147 (tppp) cc_final: 0.7692 (ttpt)
REVERT: B  151 SER cc_start: 0.8470 (m) cc_final: 0.8233 (t)
REVERT: B  207 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7999 (mtm-85)
REVERT: B  239 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8306 (tt)
REVERT: B  253 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7868 (tttm)
REVERT: B  274 GLN cc_start: 0.8950 (mt0) cc_final: 0.8584 (mt0)
REVERT: B  425 GLU cc_start: 0.7620 (mp0) cc_final: 0.7271 (mp0)
REVERT: B  479 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7509 (pp20)
REVERT: B  508 THR cc_start: 0.7368 (t) cc_final: 0.7144 (p)
REVERT: B  712 ASN cc_start: 0.8440 (t0) cc_final: 0.8048 (t0)
REVERT: B  714 SER cc_start: 0.8546 (t) cc_final: 0.8198 (t)
REVERT: B  780 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8509 (mt-10)
REVERT: B  900 MET cc_start: 0.7627 (ptp) cc_final: 0.7247 (ptt)
REVERT: B  952 GLU cc_start: 0.8171 (mp0) cc_final: 0.7348 (tp30)
REVERT: B 1026 MET cc_start: 0.6121 (mtp) cc_final: 0.5919 (mtm)
REVERT: B 1053 SER cc_start: 0.8156 (t) cc_final: 0.7424 (p)
REVERT: B 1062 LEU cc_start: 0.8355 (mt) cc_final: 0.8118 (mt)
REVERT: B 1077 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8445 (tm-30)
  outliers start: 20
  outliers final: 5
  residues processed: 377
  average time/residue: 1.2181
  time to fit residues: 528.5180
Evaluate side-chains
  258 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 250
  time to evaluate  : 2.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  449 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  241 PRO
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  782 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 212 optimal weight:    0.9990
   chunk 191 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 197 optimal weight:    0.3980
   chunk 76 optimal weight:    0.8980
   chunk 120 optimal weight:    3.9990
   chunk 147 optimal weight:    0.7980
   chunk 228 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
A 137 GLN
A 140 ASN
A 184 ASN
A 257 HIS
A 303 HIS
A 381 ASN
A 445 GLN
A 534 ASN
A 572 HIS
A 619 GLN
A 632 GLN
A 730 GLN
A 745 GLN
A 819 ASN
A 860 ASN
A 931 GLN
A 955 HIS
A1067 ASN
A1264 ASN
B 145 ASN
B 212 GLN
B 524 GLN
B 570 GLN
B 591 ASN
B 643 GLN
B 733 ASN
B 777 ASN
B 825 HIS
B 863 ASN
B 873 ASN
B 908 ASN
B1059 ASN
B1135 GLN

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  20777  Z= 0.182
  Angle     :  0.563  10.580  28139  Z= 0.309
  Chirality :  0.044   0.161   3141
  Planarity :  0.004   0.100   3624
  Dihedral  :  6.244  57.291   2751
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.87 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.27 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.15), residues: 2526
  helix: -1.51 (0.18), residues: 641
  sheet: -1.87 (0.22), residues: 481
  loop : -1.86 (0.15), residues: 1404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 629 
 HIS   0.006   0.001   HIS A 922 
 PHE   0.024   0.001   PHE B 438 
 TYR   0.018   0.001   TYR A1108 
 ARG   0.004   0.000   ARG A 553 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 296
  time to evaluate  : 2.517 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.8185 (tt0) cc_final: 0.7948 (tt0)
REVERT: A   48 ARG cc_start: 0.6909 (ptp-110) cc_final: 0.6355 (ptp-110)
REVERT: A   94 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7733 (mtm-85)
REVERT: A  383 ARG cc_start: 0.7612 (ttp80) cc_final: 0.7356 (ttt-90)
REVERT: A  447 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8437 (pt)
REVERT: A  471 GLN cc_start: 0.8121 (pp30) cc_final: 0.7736 (pp30)
REVERT: A  530 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7273 (mtm110)
REVERT: A  554 ASP cc_start: 0.8616 (t70) cc_final: 0.8352 (OUTLIER)
REVERT: A  576 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6793 (tm)
REVERT: A  593 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8423 (mm-30)
REVERT: A  615 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7462 (pt0)
REVERT: A  639 ASN cc_start: 0.8703 (m-40) cc_final: 0.8455 (m-40)
REVERT: A  653 ASP cc_start: 0.6887 (m-30) cc_final: 0.5900 (t0)
REVERT: A  691 ASP cc_start: 0.8381 (p0) cc_final: 0.8178 (p0)
REVERT: A  711 TYR cc_start: 0.7111 (t80) cc_final: 0.6796 (t80)
REVERT: A  834 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7912 (tttt)
REVERT: A  868 TYR cc_start: 0.8196 (t80) cc_final: 0.7661 (t80)
REVERT: A  876 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8450 (mtm110)
REVERT: A  971 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8176 (tttm)
REVERT: A 1209 MET cc_start: 0.5656 (ptt) cc_final: 0.4264 (tmm)
REVERT: A 1288 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7721 (tttp)
REVERT: B  207 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8004 (mtm-85)
REVERT: B  253 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7854 (tttm)
REVERT: B  274 GLN cc_start: 0.8634 (mt0) cc_final: 0.8370 (mt0)
REVERT: B  425 GLU cc_start: 0.7752 (mp0) cc_final: 0.7394 (mp0)
REVERT: B  479 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7244 (pp20)
REVERT: B  627 MET cc_start: 0.9132 (mtm) cc_final: 0.8797 (mtp)
REVERT: B  648 ILE cc_start: 0.7975 (pt) cc_final: 0.7632 (pp)
REVERT: B  712 ASN cc_start: 0.8276 (t0) cc_final: 0.7994 (t0)
REVERT: B  780 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8474 (mt-10)
REVERT: B  900 MET cc_start: 0.7319 (ptp) cc_final: 0.6884 (ptt)
REVERT: B  952 GLU cc_start: 0.8281 (mp0) cc_final: 0.7495 (tp30)
REVERT: B 1077 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8357 (tm-30)
REVERT: B 1099 TYR cc_start: 0.7954 (m-80) cc_final: 0.7668 (m-80)
  outliers start: 59
  outliers final: 20
  residues processed: 327
  average time/residue: 1.1163
  time to fit residues: 425.7904
Evaluate side-chains
  266 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 2.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  449 PHE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  593 GLU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue 1288 LYS
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  986 ASP
Chi-restraints excluded: chain B residue 1036 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 190 optimal weight:    4.9990
   chunk 155 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 229 optimal weight:    4.9990
   chunk 247 optimal weight:   20.0000
   chunk 204 optimal weight:    3.9990
   chunk 227 optimal weight:    0.8980
   chunk 78 optimal weight:    9.9990
   chunk 183 optimal weight:    0.6980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
A 303 HIS
A 534 ASN
** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
A1133 HIS
A1135 GLN
B 127 HIS
B 362 GLN
B 623 ASN
B 760 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  20777  Z= 0.383
  Angle     :  0.612   9.688  28139  Z= 0.328
  Chirality :  0.047   0.234   3141
  Planarity :  0.004   0.101   3624
  Dihedral  :  5.912  58.304   2741
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.45 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.68 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.16), residues: 2526
  helix: -0.50 (0.19), residues: 636
  sheet: -1.86 (0.21), residues: 510
  loop : -1.64 (0.16), residues: 1380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 629 
 HIS   0.004   0.001   HIS A 893 
 PHE   0.023   0.002   PHE B 438 
 TYR   0.024   0.002   TYR A  57 
 ARG   0.004   0.000   ARG A 553 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 268
  time to evaluate  : 2.394 
Fit side-chains
REVERT: A    6 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8258 (mmt)
REVERT: A   46 GLU cc_start: 0.8150 (tt0) cc_final: 0.7723 (tt0)
REVERT: A   48 ARG cc_start: 0.6991 (ptp-110) cc_final: 0.6392 (ptp-110)
REVERT: A   83 MET cc_start: 0.7619 (mpt) cc_final: 0.7383 (mmt)
REVERT: A  135 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7950 (tp30)
REVERT: A  447 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8498 (pt)
REVERT: A  471 GLN cc_start: 0.8250 (pp30) cc_final: 0.7851 (pp30)
REVERT: A  530 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7310 (mtm110)
REVERT: A  554 ASP cc_start: 0.8684 (t70) cc_final: 0.8412 (OUTLIER)
REVERT: A  576 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6776 (tm)
REVERT: A  615 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7575 (pt0)
REVERT: A  639 ASN cc_start: 0.8708 (m-40) cc_final: 0.8448 (m-40)
REVERT: A  653 ASP cc_start: 0.6995 (m-30) cc_final: 0.6022 (t0)
REVERT: A  691 ASP cc_start: 0.8446 (p0) cc_final: 0.8238 (p0)
REVERT: A  711 TYR cc_start: 0.7210 (t80) cc_final: 0.6949 (t80)
REVERT: A  834 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7889 (tptt)
REVERT: A  868 TYR cc_start: 0.8290 (t80) cc_final: 0.7807 (t80)
REVERT: A  876 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.8421 (mtm110)
REVERT: A  971 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8120 (tttm)
REVERT: A 1209 MET cc_start: 0.5627 (ptt) cc_final: 0.4256 (tmm)
REVERT: A 1276 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8171 (p)
REVERT: B   11 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7898 (ttp-170)
REVERT: B  207 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8014 (mtm-85)
REVERT: B  239 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7295 (tt)
REVERT: B  253 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7880 (tttm)
REVERT: B  274 GLN cc_start: 0.8638 (mt0) cc_final: 0.8362 (mt0)
REVERT: B  425 GLU cc_start: 0.7725 (mp0) cc_final: 0.7299 (mp0)
REVERT: B  452 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7641 (mmt)
REVERT: B  479 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7004 (pp20)
REVERT: B  627 MET cc_start: 0.9171 (mtm) cc_final: 0.8892 (mtp)
REVERT: B  648 ILE cc_start: 0.7989 (pt) cc_final: 0.7628 (pp)
REVERT: B  712 ASN cc_start: 0.8349 (t0) cc_final: 0.8037 (t0)
REVERT: B  780 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8449 (mt-10)
REVERT: B  845 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7221 (m-30)
REVERT: B  900 MET cc_start: 0.7416 (ptp) cc_final: 0.7038 (ptt)
REVERT: B  952 GLU cc_start: 0.8277 (mp0) cc_final: 0.7560 (tp30)
REVERT: B 1099 TYR cc_start: 0.7961 (m-80) cc_final: 0.7686 (m-80)
REVERT: B 1121 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7169 (tttp)
  outliers start: 82
  outliers final: 30
  residues processed: 313
  average time/residue: 1.1273
  time to fit residues: 411.2028
Evaluate side-chains
  284 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 2.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  449 PHE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  952 GLN
Chi-restraints excluded: chain A residue  958 GLN
Chi-restraints excluded: chain A residue 1276 THR
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  606 LYS
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue  949 SER
Chi-restraints excluded: chain B residue  986 ASP
Chi-restraints excluded: chain B residue 1036 THR
Chi-restraints excluded: chain B residue 1117 THR
Chi-restraints excluded: chain B residue 1121 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 226 optimal weight:    5.9990
   chunk 172 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9980
   chunk 230 optimal weight:    0.8980
   chunk 243 optimal weight:    0.4980
   chunk 120 optimal weight:    0.4980
   chunk 218 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
A 619 GLN
A 860 ASN
** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B 127 HIS
B1059 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.071  20777  Z= 0.153
  Angle     :  0.497   8.288  28139  Z= 0.270
  Chirality :  0.043   0.162   3141
  Planarity :  0.004   0.099   3624
  Dihedral  :  5.346  58.114   2741
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.48 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.16), residues: 2526
  helix:  0.36 (0.21), residues: 635
  sheet: -1.68 (0.22), residues: 487
  loop : -1.43 (0.16), residues: 1404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A 922 
 PHE   0.019   0.001   PHE B 438 
 TYR   0.017   0.001   TYR B 576 
 ARG   0.002   0.000   ARG B  40 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 290
  time to evaluate  : 2.811 
Fit side-chains
REVERT: A    6 MET cc_start: 0.8576 (mtp) cc_final: 0.8370 (mmt)
REVERT: A   46 GLU cc_start: 0.8163 (tt0) cc_final: 0.7737 (tt0)
REVERT: A   48 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6374 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8052 (tp30)
REVERT: A  447 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8229 (pt)
REVERT: A  471 GLN cc_start: 0.8250 (pp30) cc_final: 0.7760 (pp30)
REVERT: A  528 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7761 (mtp)
REVERT: A  530 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7262 (mtm110)
REVERT: A  554 ASP cc_start: 0.8524 (t70) cc_final: 0.8301 (t0)
REVERT: A  576 LEU cc_start: 0.6954 (pt) cc_final: 0.6660 (tm)
REVERT: A  615 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7556 (pt0)
REVERT: A  639 ASN cc_start: 0.8603 (m-40) cc_final: 0.8375 (m-40)
REVERT: A  653 ASP cc_start: 0.6805 (m-30) cc_final: 0.5870 (t0)
REVERT: A  691 ASP cc_start: 0.8352 (p0) cc_final: 0.8123 (p0)
REVERT: A  711 TYR cc_start: 0.7319 (t80) cc_final: 0.7029 (OUTLIER)
REVERT: A  776 MET cc_start: 0.8176 (mtp) cc_final: 0.7931 (mtm)
REVERT: A  834 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7860 (tptt)
REVERT: A  868 TYR cc_start: 0.8185 (t80) cc_final: 0.7620 (t80)
REVERT: A  876 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8372 (mtm110)
REVERT: A  971 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8176 (tttm)
REVERT: A 1209 MET cc_start: 0.5758 (ptt) cc_final: 0.4365 (tmm)
REVERT: A 1321 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7402 (tp30)
REVERT: B   11 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7890 (ttp-170)
REVERT: B  175 ILE cc_start: 0.8786 (mp) cc_final: 0.8568 (mp)
REVERT: B  207 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8026 (mtm-85)
REVERT: B  274 GLN cc_start: 0.8555 (mt0) cc_final: 0.8257 (mt0)
REVERT: B  344 ASN cc_start: 0.8553 (t0) cc_final: 0.8272 (t0)
REVERT: B  425 GLU cc_start: 0.7780 (mp0) cc_final: 0.7322 (mp0)
REVERT: B  445 GLN cc_start: 0.8409 (pt0) cc_final: 0.7904 (pt0)
REVERT: B  452 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7573 (mmt)
REVERT: B  479 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6981 (pp20)
REVERT: B  627 MET cc_start: 0.9077 (mtm) cc_final: 0.8870 (mtp)
REVERT: B  780 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: B  845 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7040 (m-30)
REVERT: B  847 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7924 (mp0)
REVERT: B  858 GLN cc_start: 0.8690 (tt0) cc_final: 0.8459 (pt0)
REVERT: B  900 MET cc_start: 0.7082 (ptp) cc_final: 0.6633 (ptt)
REVERT: B  952 GLU cc_start: 0.8302 (mp0) cc_final: 0.7600 (tp30)
  outliers start: 67
  outliers final: 21
  residues processed: 326
  average time/residue: 1.0843
  time to fit residues: 417.0731
Evaluate side-chains
  285 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 259
  time to evaluate  : 2.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  952 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  847 GLU
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  926 ILE
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue  949 SER
Chi-restraints excluded: chain B residue 1036 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 202 optimal weight:    0.7980
   chunk 138 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 181 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 207 optimal weight:    4.9990
   chunk 168 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 218 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
A1079 ASN
B 646 GLN
B1059 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  20777  Z= 0.208
  Angle     :  0.521   9.980  28139  Z= 0.278
  Chirality :  0.044   0.205   3141
  Planarity :  0.003   0.097   3624
  Dihedral  :  5.069  48.638   2737
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.27 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.15 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.16), residues: 2526
  helix:  0.64 (0.21), residues: 638
  sheet: -1.60 (0.22), residues: 506
  loop : -1.34 (0.16), residues: 1382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 629 
 HIS   0.015   0.001   HIS B 127 
 PHE   0.019   0.001   PHE B 438 
 TYR   0.019   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 383 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 273
  time to evaluate  : 2.683 
Fit side-chains
REVERT: A  135 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (mm-30)
REVERT: A  295 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7510 (tp30)
REVERT: A  329 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8155 (mm-30)
REVERT: A  447 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8221 (pt)
REVERT: A  471 GLN cc_start: 0.8269 (pp30) cc_final: 0.7713 (pp30)
REVERT: A  528 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7785 (mtp)
REVERT: A  530 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7281 (mtm110)
REVERT: A  554 ASP cc_start: 0.8543 (t70) cc_final: 0.8303 (OUTLIER)
REVERT: A  576 LEU cc_start: 0.6922 (pt) cc_final: 0.6619 (tm)
REVERT: A  615 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7649 (pt0)
REVERT: A  639 ASN cc_start: 0.8569 (m-40) cc_final: 0.8328 (m-40)
REVERT: A  653 ASP cc_start: 0.6785 (m-30) cc_final: 0.5886 (t0)
REVERT: A  691 ASP cc_start: 0.8385 (p0) cc_final: 0.8157 (p0)
REVERT: A  711 TYR cc_start: 0.7391 (t80) cc_final: 0.7092 (OUTLIER)
REVERT: A  776 MET cc_start: 0.8209 (mtp) cc_final: 0.7946 (mtm)
REVERT: A  834 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7879 (tptt)
REVERT: A  868 TYR cc_start: 0.8211 (t80) cc_final: 0.7647 (t80)
REVERT: A  876 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8387 (mtm110)
REVERT: A  971 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8186 (tttm)
REVERT: A 1209 MET cc_start: 0.5686 (ptt) cc_final: 0.4305 (tmm)
REVERT: A 1321 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7420 (tp30)
REVERT: B   11 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7877 (ttp-170)
REVERT: B   42 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6947 (mpp)
REVERT: B  175 ILE cc_start: 0.8788 (mp) cc_final: 0.8568 (mp)
REVERT: B  253 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7876 (tttm)
REVERT: B  267 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7191 (ttpp)
REVERT: B  271 GLU cc_start: 0.8009 (mp0) cc_final: 0.7688 (mp0)
REVERT: B  274 GLN cc_start: 0.8572 (mt0) cc_final: 0.8285 (mt0)
REVERT: B  344 ASN cc_start: 0.8488 (t0) cc_final: 0.8164 (t0)
REVERT: B  425 GLU cc_start: 0.7784 (mp0) cc_final: 0.7393 (mp0)
REVERT: B  452 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7624 (mmt)
REVERT: B  648 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7458 (pp)
REVERT: B  780 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8316 (mt-10)
REVERT: B  845 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7038 (m-30)
REVERT: B  858 GLN cc_start: 0.8690 (tt0) cc_final: 0.8423 (pt0)
REVERT: B  900 MET cc_start: 0.7124 (ptp) cc_final: 0.6697 (ptt)
REVERT: B  952 GLU cc_start: 0.8310 (mp0) cc_final: 0.7614 (tp30)
REVERT: B 1077 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8284 (tm-30)
  outliers start: 58
  outliers final: 29
  residues processed: 308
  average time/residue: 1.0730
  time to fit residues: 387.5441
Evaluate side-chains
  288 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 253
  time to evaluate  : 2.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  952 GLN
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue  949 SER
Chi-restraints excluded: chain B residue 1036 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 219 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 143 optimal weight:    4.9990
   chunk 60 optimal weight:    0.3980
   chunk 243 optimal weight:    0.9990
   chunk 202 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 128 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
A1067 ASN
A1079 ASN
B1059 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  20777  Z= 0.167
  Angle     :  0.493   7.924  28139  Z= 0.265
  Chirality :  0.043   0.165   3141
  Planarity :  0.003   0.096   3624
  Dihedral  :  4.836  35.361   2737
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.55 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.94 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.17), residues: 2526
  helix:  0.91 (0.21), residues: 632
  sheet: -1.48 (0.22), residues: 506
  loop : -1.25 (0.16), residues: 1388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A 922 
 PHE   0.018   0.001   PHE B 438 
 TYR   0.022   0.001   TYR A 518 
 ARG   0.003   0.000   ARG A 383 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 284
  time to evaluate  : 2.630 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.7017 (ptp-110) cc_final: 0.6405 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7985 (tp30)
REVERT: A  295 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7513 (tp30)
REVERT: A  329 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8168 (mm-30)
REVERT: A  471 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7798 (pp30)
REVERT: A  530 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7287 (mtm110)
REVERT: A  554 ASP cc_start: 0.8469 (t70) cc_final: 0.8239 (t0)
REVERT: A  576 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6590 (tm)
REVERT: A  615 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7709 (pt0)
REVERT: A  639 ASN cc_start: 0.8514 (m-40) cc_final: 0.8279 (m-40)
REVERT: A  653 ASP cc_start: 0.6683 (m-30) cc_final: 0.5827 (t0)
REVERT: A  691 ASP cc_start: 0.8349 (p0) cc_final: 0.8112 (p0)
REVERT: A  711 TYR cc_start: 0.7416 (t80) cc_final: 0.7185 (t80)
REVERT: A  776 MET cc_start: 0.8188 (mtp) cc_final: 0.7928 (mtm)
REVERT: A  834 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7834 (tptt)
REVERT: A  868 TYR cc_start: 0.8193 (t80) cc_final: 0.7600 (t80)
REVERT: A  876 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8374 (mtm110)
REVERT: A  971 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8208 (tttm)
REVERT: A 1045 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7629 (ttp-110)
REVERT: A 1209 MET cc_start: 0.5616 (ptt) cc_final: 0.4290 (tmm)
REVERT: B   11 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7829 (ttp-170)
REVERT: B   42 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7124 (mpp)
REVERT: B  156 ASN cc_start: 0.8246 (t0) cc_final: 0.7911 (t0)
REVERT: B  175 ILE cc_start: 0.8708 (mp) cc_final: 0.8417 (mp)
REVERT: B  267 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7221 (ttpp)
REVERT: B  271 GLU cc_start: 0.7986 (mp0) cc_final: 0.7680 (mp0)
REVERT: B  274 GLN cc_start: 0.8565 (mt0) cc_final: 0.8288 (mt0)
REVERT: B  344 ASN cc_start: 0.8503 (t0) cc_final: 0.8161 (t0)
REVERT: B  425 GLU cc_start: 0.7863 (mp0) cc_final: 0.7480 (mp0)
REVERT: B  452 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7610 (mmt)
REVERT: B  648 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7316 (pp)
REVERT: B  780 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8257 (mt-10)
REVERT: B  845 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6903 (m-30)
REVERT: B  847 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7898 (mp0)
REVERT: B  900 MET cc_start: 0.6983 (ptp) cc_final: 0.6569 (ptt)
REVERT: B  952 GLU cc_start: 0.8318 (mp0) cc_final: 0.7551 (tp30)
REVERT: B  953 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7897 (mt-10)
REVERT: B  954 ASN cc_start: 0.8605 (m-40) cc_final: 0.8304 (m110)
  outliers start: 65
  outliers final: 27
  residues processed: 321
  average time/residue: 1.0774
  time to fit residues: 409.0187
Evaluate side-chains
  295 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 259
  time to evaluate  : 2.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1045 ARG
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue 1036 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 235 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 178 optimal weight:    0.9980
   chunk 137 optimal weight:    0.8980
   chunk 205 optimal weight:    2.9990
   chunk 136 optimal weight:    0.6980
   chunk 242 optimal weight:    8.9990
   chunk 152 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 952 GLN
A1067 ASN
A1079 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  20777  Z= 0.232
  Angle     :  0.525   7.827  28139  Z= 0.279
  Chirality :  0.044   0.258   3141
  Planarity :  0.003   0.094   3624
  Dihedral  :  4.888  33.596   2737
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.19 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.21 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.17), residues: 2526
  helix:  0.86 (0.21), residues: 644
  sheet: -1.48 (0.23), residues: 494
  loop : -1.22 (0.16), residues: 1388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A 893 
 PHE   0.019   0.001   PHE B 438 
 TYR   0.022   0.002   TYR A 518 
 ARG   0.006   0.000   ARG A 901 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 259
  time to evaluate  : 2.419 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.7030 (ptp-110) cc_final: 0.6414 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8004 (tp30)
REVERT: A  295 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7513 (tp30)
REVERT: A  329 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: A  447 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8170 (pt)
REVERT: A  471 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7793 (pp30)
REVERT: A  530 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7290 (mtm110)
REVERT: A  554 ASP cc_start: 0.8504 (t70) cc_final: 0.8262 (OUTLIER)
REVERT: A  615 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7681 (pt0)
REVERT: A  639 ASN cc_start: 0.8541 (m-40) cc_final: 0.8300 (m-40)
REVERT: A  653 ASP cc_start: 0.6780 (m-30) cc_final: 0.5866 (t0)
REVERT: A  691 ASP cc_start: 0.8408 (p0) cc_final: 0.8168 (p0)
REVERT: A  711 TYR cc_start: 0.7440 (t80) cc_final: 0.7227 (t80)
REVERT: A  776 MET cc_start: 0.8219 (mtp) cc_final: 0.7939 (mtm)
REVERT: A  834 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7860 (tptt)
REVERT: A  868 TYR cc_start: 0.8222 (t80) cc_final: 0.7622 (t80)
REVERT: A  876 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.8355 (mtm110)
REVERT: A  958 GLN cc_start: 0.7930 (mt0) cc_final: 0.7395 (tt0)
REVERT: A  971 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8194 (tttm)
REVERT: A 1045 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7682 (ttp-110)
REVERT: A 1209 MET cc_start: 0.5539 (ptt) cc_final: 0.4253 (tmm)
REVERT: B   42 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7093 (mpp)
REVERT: B  175 ILE cc_start: 0.8703 (mp) cc_final: 0.8400 (mp)
REVERT: B  253 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7866 (tttm)
REVERT: B  267 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7222 (ttpp)
REVERT: B  271 GLU cc_start: 0.7995 (mp0) cc_final: 0.7716 (mp0)
REVERT: B  274 GLN cc_start: 0.8609 (mt0) cc_final: 0.8334 (mt0)
REVERT: B  344 ASN cc_start: 0.8581 (t0) cc_final: 0.8254 (t0)
REVERT: B  425 GLU cc_start: 0.7767 (mp0) cc_final: 0.7360 (mp0)
REVERT: B  452 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7612 (mmt)
REVERT: B  648 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7285 (pp)
REVERT: B  780 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: B  845 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6928 (m-30)
REVERT: B  847 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7942 (mp0)
REVERT: B  900 MET cc_start: 0.7113 (ptp) cc_final: 0.6702 (ptt)
REVERT: B  952 GLU cc_start: 0.8226 (mp0) cc_final: 0.7488 (tp30)
REVERT: B  954 ASN cc_start: 0.8695 (m-40) cc_final: 0.8396 (m110)
  outliers start: 61
  outliers final: 31
  residues processed: 299
  average time/residue: 1.1436
  time to fit residues: 403.1005
Evaluate side-chains
  289 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 249
  time to evaluate  : 2.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1045 ARG
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  847 GLU
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue 1036 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 150 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 145 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 154 optimal weight:    4.9990
   chunk 165 optimal weight:    8.9990
   chunk 120 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 190 optimal weight:    0.8980
   chunk 220 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 952 GLN
A1067 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  20777  Z= 0.225
  Angle     :  0.522   7.687  28139  Z= 0.278
  Chirality :  0.044   0.210   3141
  Planarity :  0.003   0.092   3624
  Dihedral  :  4.892  33.847   2737
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.69 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.17), residues: 2526
  helix:  0.94 (0.21), residues: 644
  sheet: -1.46 (0.23), residues: 494
  loop : -1.18 (0.16), residues: 1388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 629 
 HIS   0.003   0.001   HIS A1140 
 PHE   0.018   0.001   PHE B 438 
 TYR   0.019   0.001   TYR A1291 
 ARG   0.006   0.000   ARG A 901 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 263
  time to evaluate  : 2.388 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.7054 (ptp-110) cc_final: 0.6425 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8012 (tp30)
REVERT: A  295 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7524 (tp30)
REVERT: A  447 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8126 (pt)
REVERT: A  471 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7798 (pp30)
REVERT: A  530 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7288 (mtm110)
REVERT: A  554 ASP cc_start: 0.8530 (t70) cc_final: 0.8272 (OUTLIER)
REVERT: A  615 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7703 (pt0)
REVERT: A  639 ASN cc_start: 0.8544 (m-40) cc_final: 0.8298 (m-40)
REVERT: A  653 ASP cc_start: 0.6813 (m-30) cc_final: 0.5901 (t0)
REVERT: A  691 ASP cc_start: 0.8411 (p0) cc_final: 0.8171 (p0)
REVERT: A  711 TYR cc_start: 0.7467 (t80) cc_final: 0.7253 (t80)
REVERT: A  776 MET cc_start: 0.8209 (mtp) cc_final: 0.7930 (mtm)
REVERT: A  834 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7859 (tptt)
REVERT: A  868 TYR cc_start: 0.8223 (t80) cc_final: 0.7668 (t80)
REVERT: A  876 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8358 (mtm110)
REVERT: A  958 GLN cc_start: 0.7909 (mt0) cc_final: 0.7349 (tt0)
REVERT: A  971 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8191 (tttm)
REVERT: A 1045 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7669 (ttp-110)
REVERT: A 1209 MET cc_start: 0.5505 (ptt) cc_final: 0.4342 (tmm)
REVERT: B   42 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7109 (mpp)
REVERT: B  175 ILE cc_start: 0.8664 (mp) cc_final: 0.8359 (mp)
REVERT: B  253 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7847 (tttm)
REVERT: B  267 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7244 (ttpp)
REVERT: B  270 ASP cc_start: 0.8382 (m-30) cc_final: 0.7941 (m-30)
REVERT: B  271 GLU cc_start: 0.7989 (mp0) cc_final: 0.7706 (mp0)
REVERT: B  274 GLN cc_start: 0.8578 (mt0) cc_final: 0.8298 (mt0)
REVERT: B  344 ASN cc_start: 0.8594 (t0) cc_final: 0.8259 (t0)
REVERT: B  425 GLU cc_start: 0.7755 (mp0) cc_final: 0.7319 (mp0)
REVERT: B  452 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7617 (mmt)
REVERT: B  780 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8365 (mt-10)
REVERT: B  845 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6959 (m-30)
REVERT: B  847 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7933 (mp0)
REVERT: B  900 MET cc_start: 0.7125 (ptp) cc_final: 0.6717 (ptt)
REVERT: B  952 GLU cc_start: 0.8189 (mp0) cc_final: 0.7486 (tp30)
REVERT: B  954 ASN cc_start: 0.8695 (m-40) cc_final: 0.8402 (m110)
REVERT: B 1092 ASP cc_start: 0.8081 (m-30) cc_final: 0.7463 (t70)
  outliers start: 58
  outliers final: 36
  residues processed: 300
  average time/residue: 1.0819
  time to fit residues: 381.8369
Evaluate side-chains
  290 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 247
  time to evaluate  : 2.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1045 ARG
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1321 GLU
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue 1026 MET
Chi-restraints excluded: chain B residue 1036 THR
Chi-restraints excluded: chain B residue 1086 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 232 optimal weight:    3.9990
   chunk 212 optimal weight:    5.9990
   chunk 226 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 177 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0670
   chunk 204 optimal weight:    1.9990
   chunk 214 optimal weight:    0.6980
   chunk 225 optimal weight:    1.9990
   chunk 148 optimal weight:    8.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN
A 952 GLN
A1067 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  20777  Z= 0.210
  Angle     :  0.519   8.355  28139  Z= 0.276
  Chirality :  0.044   0.185   3141
  Planarity :  0.003   0.092   3624
  Dihedral  :  4.853  33.657   2737
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.95 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.82 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.17), residues: 2526
  helix:  1.08 (0.21), residues: 637
  sheet: -1.42 (0.23), residues: 497
  loop : -1.15 (0.16), residues: 1392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A1140 
 PHE   0.018   0.001   PHE B 438 
 TYR   0.021   0.001   TYR A 518 
 ARG   0.006   0.000   ARG A 901 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 256
  time to evaluate  : 2.420 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.7037 (ptp-110) cc_final: 0.6366 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7992 (tp30)
REVERT: A  295 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7515 (tp30)
REVERT: A  447 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8112 (pt)
REVERT: A  471 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7707 (pp30)
REVERT: A  530 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7273 (mtm110)
REVERT: A  554 ASP cc_start: 0.8522 (t70) cc_final: 0.8263 (t0)
REVERT: A  615 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7620 (pt0)
REVERT: A  639 ASN cc_start: 0.8537 (m-40) cc_final: 0.8288 (m-40)
REVERT: A  653 ASP cc_start: 0.6774 (m-30) cc_final: 0.5885 (t0)
REVERT: A  691 ASP cc_start: 0.8402 (p0) cc_final: 0.8162 (p0)
REVERT: A  711 TYR cc_start: 0.7482 (t80) cc_final: 0.7273 (t80)
REVERT: A  776 MET cc_start: 0.8189 (mtp) cc_final: 0.7929 (mtm)
REVERT: A  834 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7860 (tptt)
REVERT: A  868 TYR cc_start: 0.8214 (t80) cc_final: 0.7665 (t80)
REVERT: A  876 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8431 (mtm110)
REVERT: A  958 GLN cc_start: 0.7971 (mt0) cc_final: 0.7394 (tt0)
REVERT: A  971 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8203 (tttm)
REVERT: A 1045 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7683 (ttp-110)
REVERT: A 1209 MET cc_start: 0.5432 (ptt) cc_final: 0.4330 (tmm)
REVERT: B  156 ASN cc_start: 0.8276 (t0) cc_final: 0.7929 (t0)
REVERT: B  175 ILE cc_start: 0.8604 (mp) cc_final: 0.8293 (mp)
REVERT: B  253 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7847 (tttm)
REVERT: B  267 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7237 (ttpp)
REVERT: B  270 ASP cc_start: 0.8377 (m-30) cc_final: 0.7947 (m-30)
REVERT: B  271 GLU cc_start: 0.7952 (mp0) cc_final: 0.7690 (mp0)
REVERT: B  274 GLN cc_start: 0.8583 (mt0) cc_final: 0.8309 (mt0)
REVERT: B  344 ASN cc_start: 0.8592 (t0) cc_final: 0.8259 (t0)
REVERT: B  425 GLU cc_start: 0.7748 (mp0) cc_final: 0.7410 (mp0)
REVERT: B  452 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7612 (mmt)
REVERT: B  780 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8346 (mt-10)
REVERT: B  845 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6984 (m-30)
REVERT: B  847 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7914 (mp0)
REVERT: B  900 MET cc_start: 0.7101 (ptp) cc_final: 0.6696 (ptt)
REVERT: B  952 GLU cc_start: 0.8206 (mp0) cc_final: 0.7516 (tp30)
REVERT: B  954 ASN cc_start: 0.8680 (m-40) cc_final: 0.8392 (m110)
REVERT: B 1092 ASP cc_start: 0.8069 (m-30) cc_final: 0.7426 (t70)
  outliers start: 55
  outliers final: 33
  residues processed: 295
  average time/residue: 1.0524
  time to fit residues: 368.4218
Evaluate side-chains
  291 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 251
  time to evaluate  : 2.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 ASN
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1045 ARG
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1321 GLU
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue 1036 THR
Chi-restraints excluded: chain B residue 1086 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 239 optimal weight:   10.0000
   chunk 146 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 166 optimal weight:    6.9990
   chunk 251 optimal weight:    0.9980
   chunk 231 optimal weight:    0.0050
   chunk 199 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 154 optimal weight:    4.9990
   chunk 122 optimal weight:    0.3980
   chunk 158 optimal weight:    0.6980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
A 952 GLN
A1067 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.068  20777  Z= 0.151
  Angle     :  0.499  10.778  28139  Z= 0.265
  Chirality :  0.043   0.168   3141
  Planarity :  0.003   0.091   3624
  Dihedral  :  4.658  32.168   2737
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.51 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.53 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.17), residues: 2526
  helix:  1.27 (0.21), residues: 633
  sheet: -1.28 (0.23), residues: 524
  loop : -1.09 (0.17), residues: 1369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 629 
 HIS   0.005   0.001   HIS A 922 
 PHE   0.016   0.001   PHE B 438 
 TYR   0.020   0.001   TYR A 518 
 ARG   0.006   0.000   ARG A 901 

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

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

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5052 Ramachandran restraints generated.
    2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 277
  time to evaluate  : 2.407 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.7003 (ptp-110) cc_final: 0.6388 (ptp-110)
REVERT: A  135 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7963 (tp30)
REVERT: A  295 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7511 (tp30)
REVERT: A  447 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7989 (pt)
REVERT: A  471 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7642 (pp30)
REVERT: A  530 ARG cc_start: 0.7676 (mtt90) cc_final: 0.7253 (mtm110)
REVERT: A  554 ASP cc_start: 0.8438 (t70) cc_final: 0.8207 (t0)
REVERT: A  576 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6918 (tm)
REVERT: A  578 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.4840 (m-40)
REVERT: A  615 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7636 (pt0)
REVERT: A  639 ASN cc_start: 0.8486 (m-40) cc_final: 0.8260 (m-40)
REVERT: A  653 ASP cc_start: 0.6513 (m-30) cc_final: 0.5734 (t0)
REVERT: A  691 ASP cc_start: 0.8400 (p0) cc_final: 0.8152 (p0)
REVERT: A  711 TYR cc_start: 0.7461 (t80) cc_final: 0.7219 (t80)
REVERT: A  834 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7806 (tptt)
REVERT: A  868 TYR cc_start: 0.8200 (t80) cc_final: 0.7674 (t80)
REVERT: A  876 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8419 (mtm110)
REVERT: A  958 GLN cc_start: 0.7906 (mt0) cc_final: 0.7351 (tt0)
REVERT: A  971 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8247 (tttm)
REVERT: A 1045 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7603 (ttp-110)
REVERT: A 1209 MET cc_start: 0.5517 (ptt) cc_final: 0.4566 (tmt)
REVERT: B  156 ASN cc_start: 0.8156 (t0) cc_final: 0.7870 (t0)
REVERT: B  240 GLN cc_start: 0.8151 (mt0) cc_final: 0.7354 (tp-100)
REVERT: B  267 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7258 (ttpp)
REVERT: B  270 ASP cc_start: 0.8377 (m-30) cc_final: 0.7944 (m-30)
REVERT: B  271 GLU cc_start: 0.7949 (mp0) cc_final: 0.7671 (mp0)
REVERT: B  274 GLN cc_start: 0.8528 (mt0) cc_final: 0.8269 (mt0)
REVERT: B  344 ASN cc_start: 0.8514 (t0) cc_final: 0.8147 (t0)
REVERT: B  425 GLU cc_start: 0.7775 (mp0) cc_final: 0.7366 (mp0)
REVERT: B  452 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7628 (mmt)
REVERT: B  648 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7126 (pp)
REVERT: B  780 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8203 (mt-10)
REVERT: B  845 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6896 (m-30)
REVERT: B  847 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7711 (mp0)
REVERT: B  900 MET cc_start: 0.6919 (ptp) cc_final: 0.6513 (ptt)
REVERT: B  952 GLU cc_start: 0.8226 (mp0) cc_final: 0.7594 (tp30)
REVERT: B  954 ASN cc_start: 0.8625 (m-40) cc_final: 0.8375 (m110)
REVERT: B 1092 ASP cc_start: 0.8033 (m-30) cc_final: 0.7379 (t70)
  outliers start: 48
  outliers final: 26
  residues processed: 310
  average time/residue: 1.0342
  time to fit residues: 380.5003
Evaluate side-chains
  288 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 252
  time to evaluate  : 2.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1045 ARG
Chi-restraints excluded: chain A residue 1321 GLU
Chi-restraints excluded: chain A residue 1326 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  782 THR
Chi-restraints excluded: chain B residue  828 THR
Chi-restraints excluded: chain B residue  845 ASP
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  897 LEU
Chi-restraints excluded: chain B residue  937 SER
Chi-restraints excluded: chain B residue 1036 THR
Chi-restraints excluded: chain B residue 1086 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 212 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 184 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 200 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 205 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 175 optimal weight:    0.0030
   overall best weight:    1.7796

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 952 GLN
A1067 ASN
A1079 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.118418 restraints weight = 23981.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.85
r_work: 0.3263 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  20777  Z= 0.288
  Angle     :  0.572  13.451  28139  Z= 0.300
  Chirality :  0.045   0.241   3141
  Planarity :  0.004   0.089   3624
  Dihedral  :  4.895  33.779   2737
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.42 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.92 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.17), residues: 2526
  helix:  1.10 (0.21), residues: 635
  sheet: -1.33 (0.23), residues: 500
  loop : -1.09 (0.16), residues: 1391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 629 
 HIS   0.005   0.001   HIS A1140 
 PHE   0.019   0.002   PHE B 438 
 TYR   0.020   0.002   TYR A1108 
 ARG   0.007   0.000   ARG A 901 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7186.17 seconds
wall clock time: 130 minutes 3.02 seconds (7803.02 seconds total)