Starting phenix.real_space_refine
on Wed Mar 12 08:04:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2025/7ktw_23032.cif"
  }
  resolution = 4.27
  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=   0.032
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      43      5.16       5
     C    4671      2.51       5
     N    1373      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7577
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 995, 7577
          Classifications: {'peptide': 995}
          Link IDs: {'PTRANS': 35, 'TRANS': 959}
          Chain breaks: 1
  Time building chain proxies: 4.77, per 1000 atoms: 0.63
  Number of scatterers: 7577
  At special positions: 0
  Unit cell: (84.975, 97.35, 128.7, 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      43     16.00
     O    1490      8.00
     N    1373      7.00
     C    4671      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      86.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.622A  pdb=" N   GLU A  10 " --> pdb=" O   THR A   6 " (cutoff:3.500A)
      Proline residue:  A  15  - end of helix
      removed outlier: 3.578A  pdb=" N   LEU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   MET A  26 " --> pdb=" O   HIS A  22 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU A  29 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 65
      removed outlier: 3.783A  pdb=" N   VAL A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASN A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 98
      removed outlier: 4.145A  pdb=" N   ASP A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.621A  pdb=" N   ILE A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LYS A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 148
      removed outlier: 4.315A  pdb=" N   TYR A 107 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 113 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ALA A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      removed outlier: 3.509A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.683A  pdb=" N   LYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 218
      removed outlier: 3.629A  pdb=" N   MET A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.535A  pdb=" N   THR A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 249
      removed outlier: 4.243A  pdb=" N   GLU A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A 233 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ARG A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 4.550A  pdb=" N   ALA A 259 " --> pdb=" O   GLU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 286
      removed outlier: 3.946A  pdb=" N   LYS A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TRP A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 313
      removed outlier: 3.536A  pdb=" N   VAL A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 342
      removed outlier: 3.640A  pdb=" N   GLU A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 322 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 389
      removed outlier: 3.604A  pdb=" N   VAL A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   MET A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASP A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 3.896A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP A 397 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 424
      removed outlier: 3.580A  pdb=" N   ILE A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 451
      removed outlier: 3.925A  pdb=" N   ARG A 433 " --> pdb=" O   ASP A 429 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   SER A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   THR A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 448 " --> pdb=" O   LYS A 444 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ARG A 449 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 451 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.746A  pdb=" N   LYS A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN A 465 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 492 through 503
      removed outlier: 3.783A  pdb=" N   TRP A 503 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 531
      removed outlier: 3.634A  pdb=" N   GLU A 525 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 550
      removed outlier: 3.785A  pdb=" N   ASP A 540 " --> pdb=" O   PRO A 536 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   VAL A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 555
      removed outlier: 3.926A  pdb=" N   GLN A 554 " --> pdb=" O   GLN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 599
      removed outlier: 4.054A  pdb=" N   LEU A 572 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLN A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER A 579 " --> pdb=" O   GLN A 575 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LYS A 584 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA A 585 " --> pdb=" O   LYS A 581 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 586 " --> pdb=" O   ASP A 582 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLU A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.870A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 650
      removed outlier: 3.670A  pdb=" N   LYS A 639 " --> pdb=" O   ASN A 635 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU A 645 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 685
      removed outlier: 3.624A  pdb=" N   VAL A 658 " --> pdb=" O   ASN A 654 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLN A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 663 " --> pdb=" O   GLU A 659 " (cutoff:3.500A)
      Proline residue:  A 673  - end of helix
    Processing helix  chain 'A' and resid 688 through 717
      removed outlier: 3.810A  pdb=" N   ASN A 700 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN A 705 " --> pdb=" O   GLN A 701 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLU A 715 " --> pdb=" O   GLY A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 743
      removed outlier: 3.852A  pdb=" N   ASP A 724 " --> pdb=" O   LYS A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 774
      removed outlier: 3.506A  pdb=" N   LEU A 749 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 794
    Processing helix  chain 'A' and resid 794 through 805
      removed outlier: 3.887A  pdb=" N   VAL A 798 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 836
      removed outlier: 3.510A  pdb=" N   ILE A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 826 " --> pdb=" O   TYR A 822 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 827 " --> pdb=" O   ARG A 823 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 832 " --> pdb=" O   VAL A 828 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU A 833 " --> pdb=" O   ALA A 829 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 834 " --> pdb=" O   LYS A 830 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A 835 " --> pdb=" O   VAL A 831 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN A 836 " --> pdb=" O   ARG A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 976
      removed outlier: 3.808A  pdb=" N   LEU A 973 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A 975 " --> pdb=" O   GLN A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1005
      removed outlier: 3.738A  pdb=" N   ALA A 991 " --> pdb=" O   ILE A 987 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1040
      removed outlier: 3.879A  pdb=" N   LEU A1015 " --> pdb=" O   THR A1011 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE A1016 " --> pdb=" O   LYS A1012 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A1019 " --> pdb=" O   LEU A1015 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASP A1021 " --> pdb=" O   GLN A1017 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER A1026 " --> pdb=" O   ILE A1022 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A1029 " --> pdb=" O   ALA A1025 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1054
    Processing helix  chain 'A' and resid 1054 through 1074
      removed outlier: 3.868A  pdb=" N   THR A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR A1061 " --> pdb=" O   PRO A1057 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A1062 " --> pdb=" O   THR A1058 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A1063 " --> pdb=" O   ILE A1059 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A1064 " --> pdb=" O   SER A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1112
      removed outlier: 3.806A  pdb=" N   SER A1084 " --> pdb=" O   SER A1080 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A1095 " --> pdb=" O   LEU A1091 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A1103 " --> pdb=" O   MET A1099 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A1104 " --> pdb=" O   GLN A1100 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR A1105 " --> pdb=" O   SER A1101 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A1112 " --> pdb=" O   GLU A1108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1116
      removed outlier: 3.741A  pdb=" N   ILE A1116 " --> pdb=" O   SER A1113 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1113 through 1116'

    551 hydrogen bonds defined for protein.
    1653 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: 2.14

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2625
        1.34 -     1.46: 1040
        1.46 -     1.57: 3913
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 7654
  Sorted by residual:
  bond pdb=" C   ILE A1056 "
       pdb=" N   PRO A1057 "
    ideal  model  delta    sigma   weight residual
    1.337  1.368 -0.031 1.24e-02 6.50e+03 6.38e+00
  bond pdb=" C   GLN A 964 "
       pdb=" N   PRO A 965 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.34e+00
  bond pdb=" CA  THR A 710 "
       pdb=" C   THR A 710 "
    ideal  model  delta    sigma   weight residual
    1.524  1.499  0.024 1.27e-02 6.20e+03 3.64e+00
  bond pdb=" C   VAL A 102 "
       pdb=" N   PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.58e+00
  bond pdb=" C   GLU A  14 "
       pdb=" N   PRO A  15 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.30e-02 5.92e+03 3.32e+00
  ... (remaining 7649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 9841
        2.29 -     4.57: 417
        4.57 -     6.86: 47
        6.86 -     9.14: 15
        9.14 -    11.43: 5
  Bond angle restraints: 10325
  Sorted by residual:
  angle pdb=" C   ILE A 987 "
        pdb=" N   ILE A 988 "
        pdb=" CA  ILE A 988 "
      ideal   model   delta    sigma   weight residual
     120.53  130.49   -9.96 1.41e+00 5.03e-01 4.99e+01
  angle pdb=" C   LYS A 979 "
        pdb=" N   TRP A 980 "
        pdb=" CA  TRP A 980 "
      ideal   model   delta    sigma   weight residual
     121.54  131.89  -10.35 1.91e+00 2.74e-01 2.94e+01
  angle pdb=" N   GLY A 535 "
        pdb=" CA  GLY A 535 "
        pdb=" C   GLY A 535 "
      ideal   model   delta    sigma   weight residual
     112.34  120.46   -8.12 2.04e+00 2.40e-01 1.58e+01
  angle pdb=" N   GLY A 984 "
        pdb=" CA  GLY A 984 "
        pdb=" C   GLY A 984 "
      ideal   model   delta    sigma   weight residual
     111.42  116.78   -5.36 1.42e+00 4.96e-01 1.42e+01
  angle pdb=" N   THR A 697 "
        pdb=" CA  THR A 697 "
        pdb=" C   THR A 697 "
      ideal   model   delta    sigma   weight residual
     111.03  106.88    4.15 1.11e+00 8.12e-01 1.40e+01
  ... (remaining 10320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 4418
       15.12 -    30.24: 303
       30.24 -    45.35: 108
       45.35 -    60.47: 6
       60.47 -    75.59: 9
  Dihedral angle restraints: 4844
    sinusoidal: 1958
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  ASP A 511 "
           pdb=" C   ASP A 511 "
           pdb=" N   ARG A 512 "
           pdb=" CA  ARG A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  ARG A1003 "
           pdb=" C   ARG A1003 "
           pdb=" N   LEU A1004 "
           pdb=" CA  LEU A1004 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  ASN A 963 "
           pdb=" C   ASN A 963 "
           pdb=" N   GLN A 964 "
           pdb=" CA  GLN A 964 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.09   22.91     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 4841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 844
       0.051 -    0.102: 294
       0.102 -    0.153: 63
       0.153 -    0.204: 11
       0.204 -    0.255: 3
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" CG  LEU A 250 "
            pdb=" CB  LEU A 250 "
            pdb=" CD1 LEU A 250 "
            pdb=" CD2 LEU A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CG  LEU A 322 "
            pdb=" CB  LEU A 322 "
            pdb=" CD1 LEU A 322 "
            pdb=" CD2 LEU A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  VAL A   3 "
            pdb=" CA  VAL A   3 "
            pdb=" CG1 VAL A   3 "
            pdb=" CG2 VAL A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1212 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 346 "   -0.054 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO A 347 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 347 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 347 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 964 "   -0.039 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO A 965 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 965 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 965 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  42 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A  43 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1348
        2.75 -     3.29: 8626
        3.29 -     3.83: 13765
        3.83 -     4.36: 16773
        4.36 -     4.90: 24654
  Nonbonded interactions: 65166
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 121 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   HIS A 694 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLU A 143 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   LEU A 191 "
            pdb=" OG  SER A 194 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL A1069 "
            pdb=" OG1 THR A1072 "
     model   vdw
     2.277 3.040
  ... (remaining 65161 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     20.860
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071   7654  Z= 0.457
  Angle     :  1.121  11.429  10325  Z= 0.644
  Chirality :  0.054   0.255   1215
  Planarity :  0.007   0.080   1358
  Dihedral  : 12.461  75.590   2958
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.69 %
    Favored  : 96.18 %
  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: -4.61 (0.20), residues: 991
  helix: -2.98 (0.13), residues: 745
  sheet:  None (None), residues: 0
  loop : -2.47 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP A 702 
 HIS   0.018   0.004   HIS A  27 
 PHE   0.029   0.004   PHE A   4 
 TYR   0.022   0.003   TYR A 107 
 ARG   0.020   0.002   ARG A 758 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.8532 (tpm170) cc_final: 0.8268 (tpm170)
REVERT: A  113 ARG cc_start: 0.9219 (ptm160) cc_final: 0.8717 (ptp-170)
REVERT: A  137 VAL cc_start: 0.9530 (t) cc_final: 0.9222 (t)
REVERT: A  174 MET cc_start: 0.8746 (mmm) cc_final: 0.8395 (mmm)
REVERT: A  181 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8433 (mm-30)
REVERT: A  190 MET cc_start: 0.9301 (mtt) cc_final: 0.9003 (mtt)
REVERT: A  199 LYS cc_start: 0.8947 (tptp) cc_final: 0.8717 (tptp)
REVERT: A  201 LEU cc_start: 0.9649 (tp) cc_final: 0.9361 (tp)
REVERT: A  205 LEU cc_start: 0.9770 (tt) cc_final: 0.9504 (tp)
REVERT: A  237 MET cc_start: 0.9499 (mtm) cc_final: 0.8901 (ttm)
REVERT: A  245 ILE cc_start: 0.9249 (mt) cc_final: 0.8923 (mt)
REVERT: A  416 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7365 (mtp180)
REVERT: A  471 GLN cc_start: 0.8739 (pt0) cc_final: 0.8012 (pt0)
REVERT: A  498 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: A  502 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8692 (ttt-90)
REVERT: A  533 MET cc_start: 0.9493 (mtm) cc_final: 0.8977 (mtp)
REVERT: A  591 MET cc_start: 0.9096 (tpt) cc_final: 0.8728 (tpt)
REVERT: A  635 ASN cc_start: 0.9219 (m-40) cc_final: 0.8952 (m110)
REVERT: A  646 LYS cc_start: 0.9313 (mtmm) cc_final: 0.8910 (mtmm)
REVERT: A  701 GLN cc_start: 0.9372 (tp-100) cc_final: 0.9132 (tp-100)
REVERT: A  707 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8967 (tp30)
REVERT: A  748 MET cc_start: 0.9247 (mmp) cc_final: 0.9019 (mmm)
REVERT: A  784 LYS cc_start: 0.9666 (ttmm) cc_final: 0.9439 (tppt)
REVERT: A  797 MET cc_start: 0.9275 (mmm) cc_final: 0.9028 (mmp)
REVERT: A  799 MET cc_start: 0.9476 (mtt) cc_final: 0.9006 (tpt)
REVERT: A  823 ARG cc_start: 0.9272 (mpp80) cc_final: 0.8851 (mtt180)
REVERT: A  836 GLN cc_start: 0.8696 (mm110) cc_final: 0.8410 (mp10)
REVERT: A 1028 GLU cc_start: 0.9667 (tt0) cc_final: 0.9402 (tm-30)
REVERT: A 1046 ARG cc_start: 0.9239 (ttm110) cc_final: 0.8709 (mtm110)
REVERT: A 1073 MET cc_start: 0.9216 (mmt) cc_final: 0.8959 (mmm)
REVERT: A 1083 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8429 (mm-30)
REVERT: A 1090 MET cc_start: 0.9116 (mmt) cc_final: 0.8799 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2832
  time to fit residues: 81.0991
Evaluate side-chains
  167 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.4980
   chunk 75 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 57 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
A 471 GLN
A 575 GLN
A 814 GLN
A1086 GLN
A1093 HIS
A1094 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.087124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.068611 restraints weight = 33112.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.070547 restraints weight = 24021.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.072005 restraints weight = 18778.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7654  Z= 0.218
  Angle     :  0.722   7.331  10325  Z= 0.384
  Chirality :  0.041   0.142   1215
  Planarity :  0.006   0.050   1358
  Dihedral  :  5.763  19.872   1060
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  3.08 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.63 (0.23), residues: 991
  helix: -1.40 (0.15), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.43 (0.44), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 258 
 HIS   0.009   0.002   HIS A 694 
 PHE   0.018   0.003   PHE A 126 
 TYR   0.020   0.002   TYR A 107 
 ARG   0.010   0.001   ARG A 759 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 229
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.9586 (p) cc_final: 0.9355 (t)
REVERT: A  113 ARG cc_start: 0.9100 (ptm160) cc_final: 0.8222 (ptm160)
REVERT: A  174 MET cc_start: 0.9008 (mmm) cc_final: 0.8294 (mmm)
REVERT: A  176 ASP cc_start: 0.9527 (t0) cc_final: 0.8818 (t0)
REVERT: A  180 GLN cc_start: 0.9350 (mt0) cc_final: 0.9028 (mm-40)
REVERT: A  205 LEU cc_start: 0.9751 (tt) cc_final: 0.9504 (tt)
REVERT: A  237 MET cc_start: 0.9533 (mtm) cc_final: 0.9082 (mtm)
REVERT: A  240 GLU cc_start: 0.8933 (mp0) cc_final: 0.8730 (mp0)
REVERT: A  253 TRP cc_start: 0.4337 (m100) cc_final: 0.3580 (m100)
REVERT: A  331 MET cc_start: 0.8834 (ttt) cc_final: 0.8468 (ttt)
REVERT: A  424 ASP cc_start: 0.8929 (t0) cc_final: 0.8640 (m-30)
REVERT: A  431 ILE cc_start: 0.8545 (mm) cc_final: 0.8297 (mm)
REVERT: A  471 GLN cc_start: 0.8859 (pt0) cc_final: 0.8380 (pt0)
REVERT: A  533 MET cc_start: 0.9436 (mtm) cc_final: 0.9173 (mtp)
REVERT: A  645 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8943 (mt-10)
REVERT: A  662 GLN cc_start: 0.9481 (mt0) cc_final: 0.9049 (mp10)
REVERT: A  748 MET cc_start: 0.9337 (mmp) cc_final: 0.9065 (mpp)
REVERT: A  749 LEU cc_start: 0.8885 (mt) cc_final: 0.8497 (mt)
REVERT: A  799 MET cc_start: 0.9516 (mtt) cc_final: 0.9178 (tpt)
REVERT: A  823 ARG cc_start: 0.9213 (mpp80) cc_final: 0.8740 (mtt180)
REVERT: A  998 MET cc_start: 0.8517 (tpp) cc_final: 0.8133 (tpp)
REVERT: A 1029 VAL cc_start: 0.9600 (t) cc_final: 0.9372 (t)
REVERT: A 1046 ARG cc_start: 0.9324 (ttm110) cc_final: 0.8726 (mtm110)
REVERT: A 1083 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8250 (mm-30)
REVERT: A 1090 MET cc_start: 0.9174 (mmt) cc_final: 0.8830 (mmm)
  outliers start: 4
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2604
  time to fit residues: 75.3241
Evaluate side-chains
  176 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN
A 773 ASN
A 814 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.086584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.067924 restraints weight = 34418.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.069834 restraints weight = 25213.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.071299 restraints weight = 19807.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7654  Z= 0.211
  Angle     :  0.670   7.107  10325  Z= 0.350
  Chirality :  0.040   0.118   1215
  Planarity :  0.005   0.045   1358
  Dihedral  :  5.358  18.362   1060
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  3.69 %
    Favored  : 95.81 %
  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 (0.25), residues: 991
  helix: -0.52 (0.17), residues: 819
  sheet:  None (None), residues: 0
  loop : -2.01 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 253 
 HIS   0.008   0.001   HIS A 187 
 PHE   0.017   0.003   PHE A  78 
 TYR   0.021   0.001   TYR A 107 
 ARG   0.012   0.001   ARG A 759 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 217
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.9219 (mmm) cc_final: 0.8447 (mmm)
REVERT: A  176 ASP cc_start: 0.9541 (t0) cc_final: 0.9208 (t0)
REVERT: A  180 GLN cc_start: 0.9357 (mt0) cc_final: 0.8971 (mm-40)
REVERT: A  187 HIS cc_start: 0.8615 (t70) cc_final: 0.8356 (t70)
REVERT: A  201 LEU cc_start: 0.9649 (tp) cc_final: 0.9352 (tp)
REVERT: A  205 LEU cc_start: 0.9727 (tt) cc_final: 0.9375 (tt)
REVERT: A  216 LYS cc_start: 0.9299 (mmmt) cc_final: 0.9076 (tmtt)
REVERT: A  224 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9285 (mt-10)
REVERT: A  227 LEU cc_start: 0.9736 (tp) cc_final: 0.9471 (pp)
REVERT: A  237 MET cc_start: 0.9586 (mtm) cc_final: 0.9030 (ttm)
REVERT: A  245 ILE cc_start: 0.9487 (mt) cc_final: 0.9072 (mt)
REVERT: A  247 VAL cc_start: 0.9318 (t) cc_final: 0.9114 (t)
REVERT: A  253 TRP cc_start: 0.4477 (m100) cc_final: 0.3735 (m100)
REVERT: A  416 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7028 (mtp180)
REVERT: A  496 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9111 (mttt)
REVERT: A  533 MET cc_start: 0.9446 (mtm) cc_final: 0.9203 (mtp)
REVERT: A  591 MET cc_start: 0.9581 (mmm) cc_final: 0.9305 (mmm)
REVERT: A  633 PHE cc_start: 0.9310 (t80) cc_final: 0.8796 (t80)
REVERT: A  634 GLU cc_start: 0.9454 (mp0) cc_final: 0.9091 (mp0)
REVERT: A  635 ASN cc_start: 0.9261 (m110) cc_final: 0.9001 (m110)
REVERT: A  645 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8940 (mt-10)
REVERT: A  662 GLN cc_start: 0.9510 (mt0) cc_final: 0.9065 (mp10)
REVERT: A  799 MET cc_start: 0.9553 (mtt) cc_final: 0.9152 (tpt)
REVERT: A  832 ARG cc_start: 0.8772 (tpm170) cc_final: 0.8190 (tpp-160)
REVERT: A 1046 ARG cc_start: 0.9291 (ttm110) cc_final: 0.8863 (ttm110)
REVERT: A 1083 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8074 (mm-30)
REVERT: A 1090 MET cc_start: 0.9160 (mmt) cc_final: 0.8808 (mmm)
REVERT: A 1110 GLU cc_start: 0.9375 (mp0) cc_final: 0.9092 (mp0)
  outliers start: 4
  outliers final: 1
  residues processed: 218
  average time/residue: 0.2474
  time to fit residues: 68.4931
Evaluate side-chains
  169 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 34 optimal weight:    0.1980
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    4.4388

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN
A 492 HIS
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 971 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.083992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.065757 restraints weight = 35168.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.067512 restraints weight = 26170.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.068826 restraints weight = 20879.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7654  Z= 0.340
  Angle     :  0.762   8.385  10325  Z= 0.405
  Chirality :  0.043   0.207   1215
  Planarity :  0.005   0.054   1358
  Dihedral  :  5.353  18.998   1060
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 24.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.69 %
  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: -0.96 (0.25), residues: 991
  helix: -0.23 (0.17), residues: 809
  sheet:  None (None), residues: 0
  loop : -1.88 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 702 
 HIS   0.006   0.002   HIS A 527 
 PHE   0.020   0.004   PHE A 212 
 TYR   0.020   0.002   TYR A 107 
 ARG   0.007   0.001   ARG A 528 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9362 (tpp) cc_final: 0.9112 (tpt)
REVERT: A  174 MET cc_start: 0.9207 (mmm) cc_final: 0.8620 (mmm)
REVERT: A  181 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8456 (mm-30)
REVERT: A  205 LEU cc_start: 0.9727 (tt) cc_final: 0.9403 (tt)
REVERT: A  227 LEU cc_start: 0.9721 (tp) cc_final: 0.9441 (pp)
REVERT: A  237 MET cc_start: 0.9570 (mtm) cc_final: 0.9271 (mtt)
REVERT: A  245 ILE cc_start: 0.9490 (mt) cc_final: 0.9251 (mm)
REVERT: A  253 TRP cc_start: 0.4681 (m100) cc_final: 0.3845 (m100)
REVERT: A  531 ASN cc_start: 0.9163 (p0) cc_final: 0.8924 (p0)
REVERT: A  533 MET cc_start: 0.9448 (mtm) cc_final: 0.8901 (mtp)
REVERT: A  591 MET cc_start: 0.9538 (mmm) cc_final: 0.9334 (tpt)
REVERT: A  633 PHE cc_start: 0.9297 (t80) cc_final: 0.8886 (t80)
REVERT: A  635 ASN cc_start: 0.9337 (m110) cc_final: 0.9065 (m110)
REVERT: A  645 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9072 (mt-10)
REVERT: A  646 LYS cc_start: 0.9448 (mttt) cc_final: 0.8957 (mttt)
REVERT: A  662 GLN cc_start: 0.9528 (mt0) cc_final: 0.9065 (mp10)
REVERT: A  709 MET cc_start: 0.8974 (mmt) cc_final: 0.8762 (mmt)
REVERT: A  799 MET cc_start: 0.9583 (mtt) cc_final: 0.9169 (tpt)
REVERT: A  832 ARG cc_start: 0.8744 (tpm170) cc_final: 0.7967 (tpp-160)
REVERT: A  994 MET cc_start: 0.9259 (ppp) cc_final: 0.9045 (ppp)
REVERT: A 1059 ILE cc_start: 0.9312 (mp) cc_final: 0.9078 (mp)
REVERT: A 1090 MET cc_start: 0.9144 (mmt) cc_final: 0.8778 (mmm)
REVERT: A 1099 MET cc_start: 0.8758 (mmp) cc_final: 0.8456 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2537
  time to fit residues: 61.7010
Evaluate side-chains
  141 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0570
   chunk 96 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
A 369 ASN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.089296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.070208 restraints weight = 33197.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.072089 restraints weight = 24579.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.073496 restraints weight = 19524.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7654  Z= 0.195
  Angle     :  0.673   7.595  10325  Z= 0.347
  Chirality :  0.041   0.183   1215
  Planarity :  0.004   0.051   1358
  Dihedral  :  5.055  18.364   1060
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.69 %
  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: -0.44 (0.26), residues: 991
  helix:  0.14 (0.18), residues: 804
  sheet:  None (None), residues: 0
  loop : -1.71 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 702 
 HIS   0.006   0.001   HIS A 187 
 PHE   0.021   0.003   PHE A  78 
 TYR   0.022   0.001   TYR A 107 
 ARG   0.005   0.000   ARG A 132 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9289 (tpp) cc_final: 0.8972 (tpp)
REVERT: A  113 ARG cc_start: 0.9186 (ptm-80) cc_final: 0.8255 (ptm160)
REVERT: A  174 MET cc_start: 0.9115 (mmm) cc_final: 0.8891 (mmm)
REVERT: A  176 ASP cc_start: 0.9517 (t70) cc_final: 0.8924 (t70)
REVERT: A  177 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8790 (tp30)
REVERT: A  180 GLN cc_start: 0.9217 (mt0) cc_final: 0.8828 (mm-40)
REVERT: A  190 MET cc_start: 0.9478 (pmm) cc_final: 0.9229 (pmm)
REVERT: A  205 LEU cc_start: 0.9715 (tt) cc_final: 0.9326 (tt)
REVERT: A  227 LEU cc_start: 0.9734 (tp) cc_final: 0.9491 (pp)
REVERT: A  237 MET cc_start: 0.9574 (mtm) cc_final: 0.9225 (mtt)
REVERT: A  245 ILE cc_start: 0.9488 (mt) cc_final: 0.9138 (mt)
REVERT: A  533 MET cc_start: 0.9416 (mtm) cc_final: 0.9187 (mtp)
REVERT: A  593 GLN cc_start: 0.9374 (mt0) cc_final: 0.9071 (mm-40)
REVERT: A  633 PHE cc_start: 0.9187 (t80) cc_final: 0.8852 (t80)
REVERT: A  635 ASN cc_start: 0.9291 (m110) cc_final: 0.9024 (m110)
REVERT: A  645 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9010 (mt-10)
REVERT: A  646 LYS cc_start: 0.9331 (mttt) cc_final: 0.8931 (mttt)
REVERT: A  662 GLN cc_start: 0.9479 (mt0) cc_final: 0.9018 (mp10)
REVERT: A  799 MET cc_start: 0.9544 (mtt) cc_final: 0.9182 (tpt)
REVERT: A  994 MET cc_start: 0.9217 (ppp) cc_final: 0.8996 (ppp)
REVERT: A 1000 GLU cc_start: 0.9593 (tp30) cc_final: 0.9351 (tp30)
REVERT: A 1003 ARG cc_start: 0.8925 (tmt170) cc_final: 0.8656 (ptm-80)
REVERT: A 1090 MET cc_start: 0.9074 (mmt) cc_final: 0.8724 (mmm)
REVERT: A 1110 GLU cc_start: 0.9344 (mp0) cc_final: 0.9044 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2591
  time to fit residues: 69.2524
Evaluate side-chains
  160 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0030
   chunk 72 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.086947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.068155 restraints weight = 34722.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.070057 restraints weight = 25609.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.071506 restraints weight = 20296.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7654  Z= 0.217
  Angle     :  0.710   7.741  10325  Z= 0.365
  Chirality :  0.041   0.173   1215
  Planarity :  0.005   0.047   1358
  Dihedral  :  4.924  17.991   1060
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 19.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.96 %
    Favored  : 96.92 %
  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: -0.07 (0.27), residues: 991
  helix:  0.37 (0.18), residues: 801
  sheet:  None (None), residues: 0
  loop : -1.44 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 253 
 HIS   0.004   0.001   HIS A 187 
 PHE   0.019   0.002   PHE A  78 
 TYR   0.021   0.002   TYR A 107 
 ARG   0.007   0.001   ARG A 759 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 HIS cc_start: 0.8863 (t70) cc_final: 0.8522 (t70)
REVERT: A   74 MET cc_start: 0.9360 (tpp) cc_final: 0.9063 (tpt)
REVERT: A  128 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8921 (mt-10)
REVERT: A  174 MET cc_start: 0.9121 (mmm) cc_final: 0.8621 (mmm)
REVERT: A  176 ASP cc_start: 0.9540 (t70) cc_final: 0.9315 (t70)
REVERT: A  177 GLU cc_start: 0.9194 (mp0) cc_final: 0.8884 (mp0)
REVERT: A  190 MET cc_start: 0.9488 (pmm) cc_final: 0.9234 (pmm)
REVERT: A  227 LEU cc_start: 0.9742 (tp) cc_final: 0.9456 (pp)
REVERT: A  237 MET cc_start: 0.9572 (mtm) cc_final: 0.9328 (mtt)
REVERT: A  245 ILE cc_start: 0.9515 (mt) cc_final: 0.9153 (mt)
REVERT: A  407 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8678 (tm-30)
REVERT: A  533 MET cc_start: 0.9438 (mtm) cc_final: 0.9221 (mtp)
REVERT: A  587 MET cc_start: 0.6693 (mtm) cc_final: 0.6451 (mtt)
REVERT: A  589 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9133 (pt0)
REVERT: A  633 PHE cc_start: 0.9217 (t80) cc_final: 0.8915 (t80)
REVERT: A  634 GLU cc_start: 0.9477 (mp0) cc_final: 0.9204 (mp0)
REVERT: A  635 ASN cc_start: 0.9298 (m110) cc_final: 0.8973 (m110)
REVERT: A  645 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9067 (mt-10)
REVERT: A  646 LYS cc_start: 0.9334 (mttt) cc_final: 0.9102 (mttt)
REVERT: A  662 GLN cc_start: 0.9453 (mt0) cc_final: 0.8984 (mp10)
REVERT: A  701 GLN cc_start: 0.9263 (tp40) cc_final: 0.9039 (tp-100)
REVERT: A  799 MET cc_start: 0.9571 (mtt) cc_final: 0.9196 (tpt)
REVERT: A  832 ARG cc_start: 0.8744 (tpm170) cc_final: 0.8179 (tpp-160)
REVERT: A  994 MET cc_start: 0.9192 (ppp) cc_final: 0.8965 (ppp)
REVERT: A 1000 GLU cc_start: 0.9591 (tp30) cc_final: 0.9314 (tp30)
REVERT: A 1001 MET cc_start: 0.9076 (ppp) cc_final: 0.8856 (ppp)
REVERT: A 1003 ARG cc_start: 0.8938 (tmt170) cc_final: 0.8691 (ptm-80)
REVERT: A 1073 MET cc_start: 0.9414 (mmm) cc_final: 0.9193 (mmm)
REVERT: A 1081 ASP cc_start: 0.8893 (t0) cc_final: 0.8287 (p0)
REVERT: A 1110 GLU cc_start: 0.9333 (mp0) cc_final: 0.9103 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 208
  average time/residue: 0.2675
  time to fit residues: 70.3387
Evaluate side-chains
  161 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
A 369 ASN
** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 685 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.088027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.068876 restraints weight = 34363.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.070804 restraints weight = 25457.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.072263 restraints weight = 20137.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.5023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7654  Z= 0.200
  Angle     :  0.695   8.501  10325  Z= 0.356
  Chirality :  0.041   0.167   1215
  Planarity :  0.004   0.047   1358
  Dihedral  :  4.824  18.571   1060
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -0.00 (0.27), residues: 991
  helix:  0.41 (0.18), residues: 803
  sheet:  None (None), residues: 0
  loop : -1.40 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 253 
 HIS   0.004   0.001   HIS A 187 
 PHE   0.020   0.002   PHE A  78 
 TYR   0.021   0.001   TYR A 107 
 ARG   0.006   0.000   ARG A 759 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 HIS cc_start: 0.8831 (t70) cc_final: 0.8544 (t-90)
REVERT: A   74 MET cc_start: 0.9376 (tpp) cc_final: 0.9022 (tpt)
REVERT: A  113 ARG cc_start: 0.9200 (ptm-80) cc_final: 0.8216 (ptp-110)
REVERT: A  174 MET cc_start: 0.9059 (mmm) cc_final: 0.8586 (mmm)
REVERT: A  176 ASP cc_start: 0.9502 (t70) cc_final: 0.9079 (t70)
REVERT: A  177 GLU cc_start: 0.9144 (mp0) cc_final: 0.8805 (mp0)
REVERT: A  180 GLN cc_start: 0.9176 (mt0) cc_final: 0.8892 (mm-40)
REVERT: A  190 MET cc_start: 0.9476 (pmm) cc_final: 0.9195 (pmm)
REVERT: A  227 LEU cc_start: 0.9737 (tp) cc_final: 0.9442 (pp)
REVERT: A  237 MET cc_start: 0.9562 (mtm) cc_final: 0.9283 (mtt)
REVERT: A  245 ILE cc_start: 0.9528 (mt) cc_final: 0.9194 (mt)
REVERT: A  253 TRP cc_start: 0.5415 (m100) cc_final: 0.4571 (m100)
REVERT: A  407 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8673 (tm-30)
REVERT: A  479 ARG cc_start: 0.8890 (mmp80) cc_final: 0.8520 (mmm160)
REVERT: A  533 MET cc_start: 0.9385 (mtm) cc_final: 0.8838 (mtp)
REVERT: A  587 MET cc_start: 0.6834 (mtm) cc_final: 0.6548 (mtt)
REVERT: A  633 PHE cc_start: 0.9172 (t80) cc_final: 0.8925 (t80)
REVERT: A  635 ASN cc_start: 0.9255 (m110) cc_final: 0.8901 (m110)
REVERT: A  643 THR cc_start: 0.9477 (p) cc_final: 0.8278 (p)
REVERT: A  646 LYS cc_start: 0.9343 (mttt) cc_final: 0.9110 (mttt)
REVERT: A  662 GLN cc_start: 0.9431 (mt0) cc_final: 0.8921 (mp10)
REVERT: A  799 MET cc_start: 0.9563 (mtt) cc_final: 0.9153 (tpt)
REVERT: A  832 ARG cc_start: 0.8721 (tpm170) cc_final: 0.8184 (tpp-160)
REVERT: A 1000 GLU cc_start: 0.9550 (tp30) cc_final: 0.9101 (tp30)
REVERT: A 1001 MET cc_start: 0.9081 (ppp) cc_final: 0.8870 (ppp)
REVERT: A 1073 MET cc_start: 0.9162 (mmm) cc_final: 0.8910 (mmm)
REVERT: A 1090 MET cc_start: 0.8634 (mpp) cc_final: 0.8423 (mpp)
REVERT: A 1110 GLU cc_start: 0.9316 (mp0) cc_final: 0.9074 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2432
  time to fit residues: 64.0926
Evaluate side-chains
  162 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
A 369 ASN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 773 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.086996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.068010 restraints weight = 34869.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.069867 restraints weight = 25866.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.071325 restraints weight = 20564.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7654  Z= 0.218
  Angle     :  0.710  11.441  10325  Z= 0.365
  Chirality :  0.042   0.155   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  4.770  19.241   1060
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.60 %
    Favored  : 98.28 %
  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: -0.00 (0.27), residues: 991
  helix:  0.40 (0.18), residues: 804
  sheet:  None (None), residues: 0
  loop : -1.37 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 253 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.018   0.002   PHE A  78 
 TYR   0.020   0.001   TYR A 107 
 ARG   0.007   0.000   ARG A 759 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9408 (tpp) cc_final: 0.9039 (tpt)
REVERT: A  113 ARG cc_start: 0.9073 (ptm-80) cc_final: 0.8359 (ptp-170)
REVERT: A  174 MET cc_start: 0.9076 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  176 ASP cc_start: 0.9517 (t70) cc_final: 0.9285 (t70)
REVERT: A  177 GLU cc_start: 0.9174 (mp0) cc_final: 0.8856 (mp0)
REVERT: A  190 MET cc_start: 0.9391 (pmm) cc_final: 0.9186 (pmm)
REVERT: A  227 LEU cc_start: 0.9742 (tp) cc_final: 0.9446 (pp)
REVERT: A  245 ILE cc_start: 0.9547 (mt) cc_final: 0.9220 (mt)
REVERT: A  253 TRP cc_start: 0.5420 (m100) cc_final: 0.4490 (m100)
REVERT: A  479 ARG cc_start: 0.8963 (mmp80) cc_final: 0.8577 (mmm160)
REVERT: A  533 MET cc_start: 0.9409 (mtm) cc_final: 0.8986 (mtm)
REVERT: A  633 PHE cc_start: 0.9221 (t80) cc_final: 0.8908 (t80)
REVERT: A  635 ASN cc_start: 0.9149 (m110) cc_final: 0.8912 (m110)
REVERT: A  646 LYS cc_start: 0.9345 (mttt) cc_final: 0.9116 (mttt)
REVERT: A  662 GLN cc_start: 0.9459 (mt0) cc_final: 0.9189 (mp10)
REVERT: A  694 HIS cc_start: 0.9010 (t-170) cc_final: 0.8790 (t-170)
REVERT: A  702 TRP cc_start: 0.9198 (t60) cc_final: 0.8739 (t60)
REVERT: A  707 GLU cc_start: 0.9431 (mp0) cc_final: 0.9120 (mp0)
REVERT: A  799 MET cc_start: 0.9554 (mtt) cc_final: 0.9157 (tpt)
REVERT: A  832 ARG cc_start: 0.8736 (tpm170) cc_final: 0.8199 (tpp-160)
REVERT: A  994 MET cc_start: 0.9176 (ppp) cc_final: 0.8961 (ppp)
REVERT: A 1001 MET cc_start: 0.9033 (ppp) cc_final: 0.8797 (ppp)
REVERT: A 1011 THR cc_start: 0.9144 (m) cc_final: 0.8886 (p)
REVERT: A 1073 MET cc_start: 0.9233 (mmm) cc_final: 0.9014 (mmm)
REVERT: A 1110 GLU cc_start: 0.9312 (mp0) cc_final: 0.9079 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 199
  average time/residue: 0.2490
  time to fit residues: 63.4221
Evaluate side-chains
  154 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
A 279 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.088308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.069010 restraints weight = 34112.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.070933 restraints weight = 25423.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.072374 restraints weight = 20249.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.5473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7654  Z= 0.213
  Angle     :  0.745  10.299  10325  Z= 0.384
  Chirality :  0.043   0.176   1215
  Planarity :  0.004   0.048   1358
  Dihedral  :  4.817  18.326   1060
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 18.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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: -0.01 (0.27), residues: 991
  helix:  0.39 (0.18), residues: 797
  sheet:  None (None), residues: 0
  loop : -1.27 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.003   TRP A 394 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.052   0.003   PHE A 212 
 TYR   0.022   0.001   TYR A 107 
 ARG   0.006   0.000   ARG A 547 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9408 (tpp) cc_final: 0.9036 (tpt)
REVERT: A  113 ARG cc_start: 0.9066 (ptm-80) cc_final: 0.8306 (ptp-110)
REVERT: A  174 MET cc_start: 0.9063 (mmm) cc_final: 0.8587 (mmm)
REVERT: A  176 ASP cc_start: 0.9485 (t70) cc_final: 0.9239 (t70)
REVERT: A  177 GLU cc_start: 0.9143 (mp0) cc_final: 0.8805 (mp0)
REVERT: A  190 MET cc_start: 0.9375 (pmm) cc_final: 0.9153 (pmm)
REVERT: A  201 LEU cc_start: 0.9690 (tp) cc_final: 0.9411 (tp)
REVERT: A  245 ILE cc_start: 0.9541 (mt) cc_final: 0.9202 (mt)
REVERT: A  253 TRP cc_start: 0.5260 (m100) cc_final: 0.4428 (m100)
REVERT: A  369 ASN cc_start: 0.9349 (m-40) cc_final: 0.8826 (p0)
REVERT: A  479 ARG cc_start: 0.8964 (mmp80) cc_final: 0.8591 (mmm160)
REVERT: A  533 MET cc_start: 0.9401 (mtm) cc_final: 0.8986 (mtm)
REVERT: A  633 PHE cc_start: 0.9191 (t80) cc_final: 0.8871 (t80)
REVERT: A  635 ASN cc_start: 0.9130 (m110) cc_final: 0.8885 (m110)
REVERT: A  662 GLN cc_start: 0.9438 (mt0) cc_final: 0.9135 (mp10)
REVERT: A  694 HIS cc_start: 0.8988 (t-170) cc_final: 0.8760 (t-170)
REVERT: A  707 GLU cc_start: 0.9419 (mp0) cc_final: 0.9205 (mp0)
REVERT: A  759 ARG cc_start: 0.9256 (mpt180) cc_final: 0.8677 (mmt90)
REVERT: A  799 MET cc_start: 0.9568 (mtt) cc_final: 0.9163 (tpt)
REVERT: A  994 MET cc_start: 0.9170 (ppp) cc_final: 0.8957 (ppp)
REVERT: A 1011 THR cc_start: 0.9086 (m) cc_final: 0.8838 (p)
REVERT: A 1073 MET cc_start: 0.9159 (mmm) cc_final: 0.8902 (mmm)
REVERT: A 1110 GLU cc_start: 0.9313 (mp0) cc_final: 0.9075 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2405
  time to fit residues: 59.8804
Evaluate side-chains
  154 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0470
   chunk 95 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.9680

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 971 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.087066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.068342 restraints weight = 35321.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.070287 restraints weight = 26209.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.071722 restraints weight = 20671.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.5721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7654  Z= 0.206
  Angle     :  0.734   7.982  10325  Z= 0.381
  Chirality :  0.042   0.148   1215
  Planarity :  0.004   0.046   1358
  Dihedral  :  4.773  22.298   1060
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.49 %
    Favored  : 99.38 %
  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:  0.09 (0.27), residues: 991
  helix:  0.47 (0.18), residues: 803
  sheet:  None (None), residues: 0
  loop : -1.31 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 283 
 HIS   0.004   0.001   HIS A 187 
 PHE   0.043   0.003   PHE A 212 
 TYR   0.019   0.001   TYR A 107 
 ARG   0.004   0.000   ARG A 512 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9416 (tpp) cc_final: 0.9047 (tpt)
REVERT: A  113 ARG cc_start: 0.9085 (ptm-80) cc_final: 0.8400 (ptp-170)
REVERT: A  154 MET cc_start: 0.9293 (tmm) cc_final: 0.9024 (ppp)
REVERT: A  174 MET cc_start: 0.9020 (mmm) cc_final: 0.8579 (mmm)
REVERT: A  176 ASP cc_start: 0.9463 (t70) cc_final: 0.9190 (t70)
REVERT: A  177 GLU cc_start: 0.9133 (mp0) cc_final: 0.8769 (mp0)
REVERT: A  201 LEU cc_start: 0.9661 (tp) cc_final: 0.9327 (tp)
REVERT: A  227 LEU cc_start: 0.9714 (tp) cc_final: 0.9379 (pp)
REVERT: A  237 MET cc_start: 0.9315 (mtt) cc_final: 0.8915 (mmm)
REVERT: A  253 TRP cc_start: 0.5154 (m100) cc_final: 0.4135 (m100)
REVERT: A  283 TRP cc_start: 0.8801 (t60) cc_final: 0.8438 (t60)
REVERT: A  369 ASN cc_start: 0.9366 (m-40) cc_final: 0.8862 (p0)
REVERT: A  479 ARG cc_start: 0.8972 (mmp80) cc_final: 0.8618 (mmm160)
REVERT: A  533 MET cc_start: 0.9421 (mtm) cc_final: 0.9198 (mtm)
REVERT: A  633 PHE cc_start: 0.9170 (t80) cc_final: 0.8886 (t80)
REVERT: A  635 ASN cc_start: 0.9057 (m110) cc_final: 0.8813 (m110)
REVERT: A  694 HIS cc_start: 0.9010 (t-170) cc_final: 0.8778 (t-170)
REVERT: A  709 MET cc_start: 0.9099 (mmt) cc_final: 0.8823 (mmm)
REVERT: A  759 ARG cc_start: 0.9198 (mpt180) cc_final: 0.8696 (mmt90)
REVERT: A  799 MET cc_start: 0.9520 (mtt) cc_final: 0.9150 (tpt)
REVERT: A 1011 THR cc_start: 0.9048 (m) cc_final: 0.8802 (p)
REVERT: A 1073 MET cc_start: 0.9216 (mmm) cc_final: 0.8947 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2442
  time to fit residues: 61.0210
Evaluate side-chains
  155 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
A 516 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 773 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.087970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.068893 restraints weight = 35029.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.070714 restraints weight = 26339.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.072142 restraints weight = 21102.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7654  Z= 0.221
  Angle     :  0.741  11.698  10325  Z= 0.386
  Chirality :  0.042   0.202   1215
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.754  20.564   1060
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.49 %
    Favored  : 99.38 %
  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:  0.24 (0.27), residues: 991
  helix:  0.55 (0.18), residues: 801
  sheet:  None (None), residues: 0
  loop : -1.13 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 283 
 HIS   0.005   0.001   HIS A 187 
 PHE   0.018   0.003   PHE A 212 
 TYR   0.019   0.002   TYR A 107 
 ARG   0.005   0.000   ARG A 762 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2731.59 seconds
wall clock time: 48 minutes 20.22 seconds (2900.22 seconds total)