Starting phenix.real_space_refine
on Sun Jun 22 20:35:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7btp_30181/06_2025/7btp_30181.cif"
  }
  resolution = 4.01
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7905 atoms to isotropic.
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      47      5.16       5
     C   12997      2.51       5
     N    3388      2.21       5
     O    3939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 20371
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 3099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3099
          Classifications: {'peptide': 384}
          Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359}
    Chain: "A"
      Number of atoms: 8042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 992, 8042
          Classifications: {'peptide': 992}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 957}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 52
    Chain: "B"
      Number of atoms: 3739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3739
          Classifications: {'peptide': 473}
          Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 876
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 2, 'TRANS': 103}
  Restraints were copied for chains:
    C, F
  Time building chain proxies: 13.24, per 1000 atoms: 0.65
  Number of scatterers: 20371
  At special positions: 0
  Unit cell: (137.7, 149.85, 121.5, 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      47     16.00
     O    3939      8.00
     N    3388      7.00
     C   12997      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: 4.31
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4850

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 15 sheets defined
      48.3% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'E' and resid 111 through 119
      removed outlier: 4.136A  pdb=" N   ASN E 119 " --> pdb=" O   TYR E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 140
    Processing helix  chain 'E' and resid 157 through 193
      removed outlier: 4.390A  pdb=" N   ILE E 161 " --> pdb=" O   ILE E 157 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP E 191 " --> pdb=" O   ASN E 187 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU E 193 " --> pdb=" O   TYR E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 226
    Processing helix  chain 'E' and resid 253 through 258
      removed outlier: 3.890A  pdb=" N   VAL E 256 " --> pdb=" O   GLU E 253 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 307 through 318
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 354 through 369
    Processing helix  chain 'E' and resid 374 through 394
    Processing helix  chain 'A' and resid 32 through 47
    Processing helix  chain 'A' and resid 56 through 73
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 95 through 105
    Processing helix  chain 'A' and resid 128 through 132
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 178 through 180
      No H-bonds generated for 'chain 'A' and resid 178 through 180'
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 239 through 247
    Processing helix  chain 'A' and resid 249 through 260
    Processing helix  chain 'A' and resid 273 through 291
      removed outlier: 3.547A  pdb=" N   ALA A 279 " --> pdb=" O   TYR A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 326
      removed outlier: 4.340A  pdb=" N   THR A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 326 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 350
      removed outlier: 3.571A  pdb=" N   TYR A 350 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 373
    Processing helix  chain 'A' and resid 383 through 393
    Processing helix  chain 'A' and resid 396 through 401
      removed outlier: 3.554A  pdb=" N   TYR A 399 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN A 400 " --> pdb=" O   PRO A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 426
      removed outlier: 3.628A  pdb=" N   GLN A 419 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS A 420 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.548A  pdb=" N   ALA A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.546A  pdb=" N   THR A 491 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU A 492 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 488 through 492'
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 509 through 528
      removed outlier: 5.727A  pdb=" N   ARG A 525 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLN A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 569
      removed outlier: 3.972A  pdb=" N   ALA A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU A 562 " --> pdb=" O   LYS A 558 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS A 567 " --> pdb=" O   GLU A 563 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   SER A 568 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 569 " --> pdb=" O   ALA A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 604
      removed outlier: 3.975A  pdb=" N   MET A 604 " --> pdb=" O   THR A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 624
      removed outlier: 3.693A  pdb=" N   LYS A 609 " --> pdb=" O   ASP A 605 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   HIS A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 645
      removed outlier: 4.000A  pdb=" N   GLN A 643 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 687
      removed outlier: 3.601A  pdb=" N   GLN A 684 " --> pdb=" O   HIS A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 718
      removed outlier: 3.832A  pdb=" N   LEU A 718 " --> pdb=" O   ASP A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 729
      removed outlier: 3.613A  pdb=" N   LEU A 729 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 739
    Processing helix  chain 'A' and resid 752 through 761
      removed outlier: 3.557A  pdb=" N   GLU A 760 " --> pdb=" O   VAL A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 793
      removed outlier: 4.119A  pdb=" N   GLU A 784 " --> pdb=" O   LYS A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 804
    Processing helix  chain 'A' and resid 805 through 807
      No H-bonds generated for 'chain 'A' and resid 805 through 807'
    Processing helix  chain 'A' and resid 811 through 823
    Processing helix  chain 'A' and resid 825 through 835
    Processing helix  chain 'A' and resid 839 through 857
    Processing helix  chain 'A' and resid 880 through 885
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 910 through 918
      removed outlier: 3.541A  pdb=" N   LYS A 915 " --> pdb=" O   ILE A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 921
      No H-bonds generated for 'chain 'A' and resid 919 through 921'
    Processing helix  chain 'A' and resid 926 through 936
      removed outlier: 4.083A  pdb=" N   LEU A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 943
    Processing helix  chain 'A' and resid 945 through 971
      removed outlier: 3.886A  pdb=" N   ILE A 949 " --> pdb=" O   ASP A 945 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ILE A 950 " --> pdb=" O   LYS A 946 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ASP A 951 " --> pdb=" O   ALA A 947 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 963 " --> pdb=" O   ARG A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 990
    Processing helix  chain 'A' and resid 999 through 1003
    Processing helix  chain 'A' and resid 1014 through 1031
      removed outlier: 3.866A  pdb=" N   GLN A1018 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.556A  pdb=" N   VAL B  23 " --> pdb=" O   ILE B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 55
      removed outlier: 3.651A  pdb=" N   PHE B  32 " --> pdb=" O   ASP B  28 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN B  34 " --> pdb=" O   TRP B  30 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TYR B  35 " --> pdb=" O   ASP B  31 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER B  50 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA B  55 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 92
      removed outlier: 3.505A  pdb=" N   SER B  89 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.991A  pdb=" N   SER B 118 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 126
      removed outlier: 3.610A  pdb=" N   SER B 125 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 164
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 3.547A  pdb=" N   GLU B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B 186 " --> pdb=" O   GLU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 214
    Processing helix  chain 'B' and resid 231 through 239
      removed outlier: 4.228A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B 238 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 270
      removed outlier: 3.612A  pdb=" N   ASN B 261 " --> pdb=" O   HIS B 257 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   HIS B 270 " --> pdb=" O   ASN B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 320
    Processing helix  chain 'B' and resid 323 through 327
    Processing helix  chain 'B' and resid 335 through 344
      removed outlier: 3.786A  pdb=" N   PHE B 339 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL B 340 " --> pdb=" O   ASP B 336 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B 341 " --> pdb=" O   PHE B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.686A  pdb=" N   GLU B 368 " --> pdb=" O   ARG B 364 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LYS B 370 " --> pdb=" O   GLY B 366 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   ILE B 371 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASN B 378 " --> pdb=" O   TYR B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 445
      removed outlier: 4.145A  pdb=" N   SER B 445 " --> pdb=" O   GLN B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 484 through 508
      removed outlier: 3.866A  pdb=" N   LEU B 488 " --> pdb=" O   ASP B 484 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ASN B 489 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   ALA B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 23
      removed outlier: 3.556A  pdb=" N   VAL C  23 " --> pdb=" O   ILE C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 55
      removed outlier: 3.651A  pdb=" N   PHE C  32 " --> pdb=" O   ASP C  28 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN C  34 " --> pdb=" O   TRP C  30 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TYR C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA C  55 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 92
      removed outlier: 3.506A  pdb=" N   SER C  89 " --> pdb=" O   PHE C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 114 through 121
      removed outlier: 3.991A  pdb=" N   SER C 118 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 126
      removed outlier: 3.611A  pdb=" N   SER C 125 " --> pdb=" O   GLY C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 164
    Processing helix  chain 'C' and resid 175 through 177
      No H-bonds generated for 'chain 'C' and resid 175 through 177'
    Processing helix  chain 'C' and resid 178 through 186
      removed outlier: 3.548A  pdb=" N   GLU C 182 " --> pdb=" O   GLY C 178 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER C 186 " --> pdb=" O   GLU C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 214
    Processing helix  chain 'C' and resid 231 through 239
      removed outlier: 4.228A  pdb=" N   ALA C 237 " --> pdb=" O   LEU C 233 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 270
      removed outlier: 3.612A  pdb=" N   ASN C 261 " --> pdb=" O   HIS C 257 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   HIS C 270 " --> pdb=" O   ASN C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 320
    Processing helix  chain 'C' and resid 323 through 327
    Processing helix  chain 'C' and resid 335 through 344
      removed outlier: 3.787A  pdb=" N   PHE C 339 " --> pdb=" O   ALA C 335 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL C 340 " --> pdb=" O   ASP C 336 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU C 341 " --> pdb=" O   PHE C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 378
      removed outlier: 3.687A  pdb=" N   GLU C 368 " --> pdb=" O   ARG C 364 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LYS C 370 " --> pdb=" O   GLY C 366 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   ILE C 371 " --> pdb=" O   ALA C 367 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASN C 378 " --> pdb=" O   TYR C 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 435 through 445
      removed outlier: 4.145A  pdb=" N   SER C 445 " --> pdb=" O   GLN C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 464
    Processing helix  chain 'C' and resid 484 through 508
      removed outlier: 3.866A  pdb=" N   LEU C 488 " --> pdb=" O   ASP C 484 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ASN C 489 " --> pdb=" O   ILE C 485 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   ALA C 490 " --> pdb=" O   ALA C 486 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE C 499 " --> pdb=" O   THR C 495 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 26
      removed outlier: 3.845A  pdb=" N   VAL D  10 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 45
      removed outlier: 4.048A  pdb=" N   ASP D  42 " --> pdb=" O   HIS D  38 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN D  43 " --> pdb=" O   MET D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 57
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 76 through 101
    Processing helix  chain 'F' and resid 6 through 26
      removed outlier: 3.845A  pdb=" N   VAL F  10 " --> pdb=" O   THR F   6 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 45
      removed outlier: 4.047A  pdb=" N   ASP F  42 " --> pdb=" O   HIS F  38 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN F  43 " --> pdb=" O   MET F  39 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 57
    Processing helix  chain 'F' and resid 67 through 71
    Processing helix  chain 'F' and resid 76 through 101
    Processing sheet with id=AA1, first strand: chain 'E' and resid 17 through 20
    Processing sheet with id=AA2, first strand: chain 'E' and resid 26 through 28
      removed outlier: 3.650A  pdb=" N   LYS E  99 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 202 through 205
      removed outlier: 3.843A  pdb=" N   GLU E 202 " --> pdb=" O   VAL E 348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 249 through 251
      removed outlier: 4.621A  pdb=" N   ASP E 249 " --> pdb=" O   TRP E 233 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 284 through 287
    Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51
      removed outlier: 6.328A  pdb=" N   GLU A  50 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   GLN A 138 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL A 152 " --> pdb=" O   GLN A 163 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLN A 163 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 154 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 113
      removed outlier: 3.937A  pdb=" N   ARG A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 264
      removed outlier: 4.141A  pdb=" N   THR A 268 " --> pdb=" O   ASP A 264 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 382
      removed outlier: 6.537A  pdb=" N   LYS A 332 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   ILE A 406 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   PHE A 334 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   TYR A 304 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   SER A 460 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP A 306 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 479
      removed outlier: 7.079A  pdb=" N   LYS A 474 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ILE A 702 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   LYS A 476 " --> pdb=" O   ILE A 702 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   THR A 704 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ASP A 478 " --> pdb=" O   THR A 704 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASN A 669 " --> pdb=" O   ASN A 701 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL A 703 " --> pdb=" O   ASN A 669 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU A 671 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASN A 539 " --> pdb=" O   LEU A 668 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR A 670 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 653 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   VAL A 655 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A 542 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ALA A 577 " --> pdb=" O   ILE A 654 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 741
    Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226
    Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 300
      removed outlier: 6.392A  pdb=" N   PHE B 296 " --> pdb=" O   SER B 348 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   LYS B 350 " --> pdb=" O   PHE B 296 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA B 298 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ARG B 352 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL B 300 " --> pdb=" O   ARG B 352 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   SER B 405 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   VAL B 381 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 413 " --> pdb=" O   GLU B 382 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL B 384 " --> pdb=" O   VAL B 413 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 224 through 226
    Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 300
      removed outlier: 6.391A  pdb=" N   PHE C 296 " --> pdb=" O   SER C 348 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   LYS C 350 " --> pdb=" O   PHE C 296 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ALA C 298 " --> pdb=" O   LYS C 350 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ARG C 352 " --> pdb=" O   ALA C 298 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL C 300 " --> pdb=" O   ARG C 352 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ALA C 354 " --> pdb=" O   VAL C 300 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   SER C 405 " --> pdb=" O   VAL C 381 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   VAL C 381 " --> pdb=" O   SER C 405 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL C 413 " --> pdb=" O   GLU C 382 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL C 384 " --> pdb=" O   VAL C 413 " (cutoff:3.500A)

    825 hydrogen bonds defined for protein.
    2352 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: 6.84

  Time building geometry restraints manager: 5.29 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: 6565
        1.34 -     1.46: 4291
        1.46 -     1.58: 9839
        1.58 -     1.70: 0
        1.70 -     1.82: 85
  Bond restraints: 20780
  Sorted by residual:
  bond pdb=" C   LEU E 121 "
       pdb=" N   PRO E 122 "
    ideal  model  delta    sigma   weight residual
    1.332  1.351 -0.019 8.20e-03 1.49e+04 5.27e+00
  bond pdb=" CA  ARG B 142 "
       pdb=" C   ARG B 142 "
    ideal  model  delta    sigma   weight residual
    1.528  1.553 -0.025 1.18e-02 7.18e+03 4.50e+00
  bond pdb=" CA  ARG C 142 "
       pdb=" C   ARG C 142 "
    ideal  model  delta    sigma   weight residual
    1.528  1.552 -0.024 1.18e-02 7.18e+03 4.10e+00
  bond pdb=" C   THR C 409 "
       pdb=" N   ASP C 410 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.40e-02 5.10e+03 3.78e+00
  bond pdb=" C   THR B 409 "
       pdb=" N   ASP B 410 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.40e-02 5.10e+03 3.70e+00
  ... (remaining 20775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 27405
        3.01 -     6.02: 588
        6.02 -     9.03: 94
        9.03 -    12.04: 17
       12.04 -    15.05: 2
  Bond angle restraints: 28106
  Sorted by residual:
  angle pdb=" C   THR B 395 "
        pdb=" N   THR B 396 "
        pdb=" CA  THR B 396 "
      ideal   model   delta    sigma   weight residual
     121.70  132.35  -10.65 1.80e+00 3.09e-01 3.50e+01
  angle pdb=" C   THR C 395 "
        pdb=" N   THR C 396 "
        pdb=" CA  THR C 396 "
      ideal   model   delta    sigma   weight residual
     121.70  132.34  -10.64 1.80e+00 3.09e-01 3.50e+01
  angle pdb=" C   THR C 409 "
        pdb=" N   ASP C 410 "
        pdb=" CA  ASP C 410 "
      ideal   model   delta    sigma   weight residual
     121.70  132.11  -10.41 1.80e+00 3.09e-01 3.34e+01
  angle pdb=" C   THR B 409 "
        pdb=" N   ASP B 410 "
        pdb=" CA  ASP B 410 "
      ideal   model   delta    sigma   weight residual
     121.70  132.07  -10.37 1.80e+00 3.09e-01 3.32e+01
  angle pdb=" C   THR A  26 "
        pdb=" N   GLY A  27 "
        pdb=" CA  GLY A  27 "
      ideal   model   delta    sigma   weight residual
     121.70  131.59   -9.89 1.80e+00 3.09e-01 3.02e+01
  ... (remaining 28101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.75: 11520
       15.75 -    31.51: 777
       31.51 -    47.26: 168
       47.26 -    63.01: 6
       63.01 -    78.76: 18
  Dihedral angle restraints: 12489
    sinusoidal: 5010
      harmonic: 7479
  Sorted by residual:
  dihedral pdb=" CA  ARG A 678 "
           pdb=" C   ARG A 678 "
           pdb=" N   TYR A 679 "
           pdb=" CA  TYR A 679 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.31  -46.69     0      5.00e+00 4.00e-02 8.72e+01
  dihedral pdb=" CA  VAL B 474 "
           pdb=" C   VAL B 474 "
           pdb=" N   GLU B 475 "
           pdb=" CA  GLU B 475 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.68   46.32     0      5.00e+00 4.00e-02 8.58e+01
  dihedral pdb=" CA  VAL C 474 "
           pdb=" C   VAL C 474 "
           pdb=" N   GLU C 475 "
           pdb=" CA  GLU C 475 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.75   46.25     0      5.00e+00 4.00e-02 8.56e+01
  ... (remaining 12486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 2399
       0.069 -    0.138: 629
       0.138 -    0.206: 66
       0.206 -    0.275: 15
       0.275 -    0.344: 5
  Chirality restraints: 3114
  Sorted by residual:
  chirality pdb=" CB  ILE A 378 "
            pdb=" CA  ILE A 378 "
            pdb=" CG1 ILE A 378 "
            pdb=" CG2 ILE A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CB  ILE B  79 "
            pdb=" CA  ILE B  79 "
            pdb=" CG1 ILE B  79 "
            pdb=" CG2 ILE B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CB  ILE C  79 "
            pdb=" CA  ILE C  79 "
            pdb=" CG1 ILE C  79 "
            pdb=" CG2 ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.43e+00
  ... (remaining 3111 not shown)

  Planarity restraints: 3646
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E  72 "   -0.066 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO E  73 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO E  73 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO E  73 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1007 "   -0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO A1008 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A1008 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A1008 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 765 "   -0.051 5.00e-02 4.00e+02   7.86e-02 9.88e+00
        pdb=" N   PRO A 766 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 766 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 766 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 3643 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 3179
        2.76 -     3.29: 19815
        3.29 -     3.83: 33595
        3.83 -     4.36: 38405
        4.36 -     4.90: 62850
  Nonbonded interactions: 157844
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F   7 "
            pdb=" OD2 ASP F  92 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR D   7 "
            pdb=" OD2 ASP D  92 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   ALA E 255 "
            pdb=" OG  SER E 259 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   PRO A1008 "
            pdb=" OH  TYR C  84 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   LEU A 342 "
            pdb=" OG1 THR A 346 "
     model   vdw
     2.272 3.040
  ... (remaining 157839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.150
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.130
  Set scattering table:                    0.180
  Process input model:                     46.170
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
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   0.076  20780  Z= 0.333
  Angle     :  1.118  15.047  28106  Z= 0.608
  Chirality :  0.061   0.344   3114
  Planarity :  0.007   0.101   3646
  Dihedral  : 11.602  78.762   7639
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 11.63 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  5.33 %
    Favored  : 94.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 1.41 %
    Twisted General : 0.41 %

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: -4.46 (0.13), residues: 2502
  helix: -2.31 (0.12), residues: 1077
  sheet: -2.73 (0.28), residues: 238
  loop : -3.68 (0.14), residues: 1187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.004   TRP E 117 
 HIS   0.011   0.003   HIS E 313 
 PHE   0.026   0.003   PHE A 599 
 TYR   0.039   0.003   TYR C 260 
 ARG   0.011   0.001   ARG A 841 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16611 (  825)
  hydrogen bonds       : angle       7.15437 ( 2352)
  covalent geometry    : bond        0.00700 (20780)
  covalent geometry    : angle       1.11843 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 373
  time to evaluate  : 2.156 
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: E  217 THR cc_start: 0.5013 (m) cc_final: 0.4501 (m)
REVERT: A  212 PHE cc_start: 0.7129 (m-80) cc_final: 0.6857 (m-80)
REVERT: A  252 THR cc_start: 0.9145 (m) cc_final: 0.8723 (t)
REVERT: A  315 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8705 (tt)
REVERT: A  589 ASN cc_start: 0.6635 (p0) cc_final: 0.5413 (p0)
REVERT: A  701 ASN cc_start: 0.8362 (m-40) cc_final: 0.8104 (m110)
REVERT: B  235 LEU cc_start: 0.7910 (tt) cc_final: 0.7329 (tp)
REVERT: B  262 LEU cc_start: 0.9214 (pp) cc_final: 0.8886 (pp)
REVERT: B  436 ILE cc_start: 0.8434 (pp) cc_final: 0.8193 (pt)
REVERT: B  440 MET cc_start: 0.7997 (tpt) cc_final: 0.7754 (tpt)
REVERT: C  201 THR cc_start: 0.7087 (m) cc_final: 0.6700 (p)
REVERT: C  223 ILE cc_start: 0.9213 (tt) cc_final: 0.9009 (mt)
REVERT: D   15 TYR cc_start: 0.8056 (t80) cc_final: 0.7640 (t80)
REVERT: D   48 TYR cc_start: 0.6981 (m-80) cc_final: 0.6687 (m-80)
REVERT: D   79 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8510 (mmm-85)
  outliers start: 13
  outliers final: 1
  residues processed: 384
  average time/residue: 0.3833
  time to fit residues: 213.2966
Evaluate side-chains
  165 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 2.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 211 optimal weight:    3.9990
   chunk 190 optimal weight:    6.9990
   chunk 105 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 128 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9990
   chunk 196 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0050
   chunk 119 optimal weight:    2.9990
   chunk 146 optimal weight:    0.8980
   chunk 227 optimal weight:    1.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  91 ASN
A 251 HIS
A 522 ASN
A 588 GLN
A 635 GLN
A 701 ASN
B 219 HIS
B 373 GLN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 ASN
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 219 HIS
C 373 GLN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 427 ASN
C 479 ASN
D  13 HIS
D  88 GLN
F  13 HIS
F  43 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.082775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.060966 restraints weight = 110956.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.062540 restraints weight = 64604.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.063594 restraints weight = 45626.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  20780  Z= 0.140
  Angle     :  0.704   8.876  28106  Z= 0.376
  Chirality :  0.046   0.209   3114
  Planarity :  0.005   0.083   3646
  Dihedral  :  6.813  37.724   2730
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 1.41 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.15), residues: 2502
  helix: -0.76 (0.14), residues: 1124
  sheet: -2.35 (0.29), residues: 267
  loop : -3.45 (0.16), residues: 1111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP E 117 
 HIS   0.006   0.001   HIS B 270 
 PHE   0.019   0.002   PHE C 199 
 TYR   0.021   0.002   TYR C 260 
 ARG   0.017   0.001   ARG B 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  825)
  hydrogen bonds       : angle       5.15977 ( 2352)
  covalent geometry    : bond        0.00289 (20780)
  covalent geometry    : angle       0.70417 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 234
  time to evaluate  : 2.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  184 LYS cc_start: 0.7808 (tttp) cc_final: 0.7577 (ttpt)
REVERT: E  314 MET cc_start: 0.7832 (tpt) cc_final: 0.7381 (mmm)
REVERT: A  136 ILE cc_start: 0.9396 (mm) cc_final: 0.9151 (mm)
REVERT: A  589 ASN cc_start: 0.6688 (p0) cc_final: 0.5896 (p0)
REVERT: A  910 MET cc_start: 0.7739 (mmp) cc_final: 0.6784 (mmp)
REVERT: B   32 PHE cc_start: 0.7235 (m-10) cc_final: 0.6991 (m-80)
REVERT: B  136 PHE cc_start: 0.8250 (t80) cc_final: 0.7793 (t80)
REVERT: C   37 LEU cc_start: 0.9474 (mt) cc_final: 0.9254 (mp)
REVERT: C   41 PHE cc_start: 0.8942 (t80) cc_final: 0.8685 (t80)
REVERT: C  223 ILE cc_start: 0.9155 (tt) cc_final: 0.8731 (mp)
REVERT: C  275 ASP cc_start: 0.8109 (p0) cc_final: 0.7668 (p0)
REVERT: C  281 LEU cc_start: 0.9219 (tp) cc_final: 0.8967 (tp)
REVERT: C  377 ASP cc_start: 0.9005 (t0) cc_final: 0.8724 (t70)
REVERT: C  440 MET cc_start: 0.8405 (tpt) cc_final: 0.8110 (tpp)
REVERT: D   12 ASP cc_start: 0.9136 (m-30) cc_final: 0.8922 (m-30)
REVERT: D   17 MET cc_start: 0.8385 (ttm) cc_final: 0.8141 (ttm)
REVERT: D   48 TYR cc_start: 0.6680 (m-80) cc_final: 0.6112 (m-80)
REVERT: D   55 VAL cc_start: 0.8807 (p) cc_final: 0.8550 (m)
REVERT: D   79 ARG cc_start: 0.9184 (mmt90) cc_final: 0.8731 (mmm-85)
REVERT: F   10 VAL cc_start: 0.9127 (t) cc_final: 0.8845 (p)
REVERT: F   89 LEU cc_start: 0.9546 (mm) cc_final: 0.9316 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 236
  average time/residue: 0.3273
  time to fit residues: 118.0809
Evaluate side-chains
  149 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 2.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 210 optimal weight:    0.0000
   chunk 230 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 145 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 219 optimal weight:    9.9990
   chunk 152 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 194 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 141 optimal weight:    8.9990
   overall best weight:    1.2790

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 726 ASN
B  21 ASN
B 244 HIS
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F   8 ASN
F  43 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.081145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.059403 restraints weight = 110069.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.060926 restraints weight = 65313.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.061936 restraints weight = 46568.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  20780  Z= 0.139
  Angle     :  0.662   8.843  28106  Z= 0.351
  Chirality :  0.045   0.214   3114
  Planarity :  0.005   0.070   3646
  Dihedral  :  6.123  35.472   2730
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  4.69 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 1.41 %
    Twisted General : 0.25 %

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: -2.31 (0.16), residues: 2502
  helix:  0.04 (0.15), residues: 1115
  sheet: -1.99 (0.31), residues: 247
  loop : -3.15 (0.16), residues: 1140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP E 117 
 HIS   0.007   0.001   HIS E 313 
 PHE   0.024   0.001   PHE C  41 
 TYR   0.022   0.002   TYR C 363 
 ARG   0.013   0.001   ARG E 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  825)
  hydrogen bonds       : angle       4.74879 ( 2352)
  covalent geometry    : bond        0.00293 (20780)
  covalent geometry    : angle       0.66205 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 2.180 
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: E  117 TRP cc_start: 0.7667 (m-90) cc_final: 0.7436 (m-90)
REVERT: E  181 MET cc_start: 0.9188 (ptm) cc_final: 0.8794 (ppp)
REVERT: E  184 LYS cc_start: 0.8035 (tttp) cc_final: 0.7773 (ttpt)
REVERT: E  314 MET cc_start: 0.7895 (tpt) cc_final: 0.7492 (mmm)
REVERT: E  379 ILE cc_start: 0.9591 (mm) cc_final: 0.9320 (mm)
REVERT: A  344 TYR cc_start: 0.8887 (t80) cc_final: 0.8680 (t80)
REVERT: A  350 TYR cc_start: 0.8032 (m-10) cc_final: 0.7806 (m-10)
REVERT: A  390 MET cc_start: 0.8971 (ttm) cc_final: 0.8649 (ttm)
REVERT: A  683 MET cc_start: 0.7438 (ptt) cc_final: 0.7216 (ptt)
REVERT: A  994 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7553 (tt0)
REVERT: B  141 ASN cc_start: 0.7655 (t0) cc_final: 0.7422 (t0)
REVERT: B  254 GLU cc_start: 0.7855 (tp30) cc_final: 0.7303 (tm-30)
REVERT: C   37 LEU cc_start: 0.9560 (mt) cc_final: 0.9347 (mp)
REVERT: C  181 TYR cc_start: 0.8049 (t80) cc_final: 0.7743 (t80)
REVERT: C  223 ILE cc_start: 0.9073 (tt) cc_final: 0.8798 (mp)
REVERT: C  275 ASP cc_start: 0.8167 (p0) cc_final: 0.7743 (p0)
REVERT: C  440 MET cc_start: 0.8474 (tpt) cc_final: 0.8175 (tpp)
REVERT: D   15 TYR cc_start: 0.8862 (t80) cc_final: 0.8636 (t80)
REVERT: D   17 MET cc_start: 0.8414 (ttm) cc_final: 0.8176 (ttm)
REVERT: D   48 TYR cc_start: 0.7166 (m-80) cc_final: 0.6890 (m-80)
REVERT: D   55 VAL cc_start: 0.8969 (p) cc_final: 0.8746 (m)
REVERT: D   79 ARG cc_start: 0.9127 (mmt90) cc_final: 0.8666 (mmm-85)
REVERT: D  102 ASN cc_start: 0.8382 (m-40) cc_final: 0.8174 (p0)
REVERT: F  104 TYR cc_start: 0.7698 (t80) cc_final: 0.7447 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2884
  time to fit residues: 87.6753
Evaluate side-chains
  126 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 2.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 237 optimal weight:    0.9980
   chunk 214 optimal weight:    5.9990
   chunk 132 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0270
   chunk 104 optimal weight:    0.0270
   chunk 249 optimal weight:    0.9980
   chunk 131 optimal weight:    7.9990
   chunk 29 optimal weight:    0.1980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
A 459 HIS
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 373 GLN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  43 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.082238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.060500 restraints weight = 111692.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.062078 restraints weight = 64905.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.063137 restraints weight = 45999.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  20780  Z= 0.116
  Angle     :  0.637   8.917  28106  Z= 0.333
  Chirality :  0.044   0.213   3114
  Planarity :  0.004   0.068   3646
  Dihedral  :  5.781  33.843   2730
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.91 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.91 (0.16), residues: 2502
  helix:  0.41 (0.16), residues: 1123
  sheet: -1.84 (0.32), residues: 239
  loop : -2.97 (0.17), residues: 1140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP E 117 
 HIS   0.005   0.001   HIS E 313 
 PHE   0.016   0.001   PHE B 362 
 TYR   0.014   0.001   TYR C 181 
 ARG   0.009   0.000   ARG A 989 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  825)
  hydrogen bonds       : angle       4.54138 ( 2352)
  covalent geometry    : bond        0.00232 (20780)
  covalent geometry    : angle       0.63729 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 2.499 
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: E  181 MET cc_start: 0.8967 (ptm) cc_final: 0.8499 (ppp)
REVERT: E  314 MET cc_start: 0.7883 (tpt) cc_final: 0.7427 (mmm)
REVERT: E  383 GLN cc_start: 0.9398 (pt0) cc_final: 0.9124 (pp30)
REVERT: A   17 LEU cc_start: 0.9075 (mm) cc_final: 0.8441 (tp)
REVERT: A  344 TYR cc_start: 0.8940 (t80) cc_final: 0.8642 (t80)
REVERT: A  390 MET cc_start: 0.8889 (ttm) cc_final: 0.8633 (ttm)
REVERT: A  658 MET cc_start: 0.8667 (mmt) cc_final: 0.8276 (mpp)
REVERT: A  683 MET cc_start: 0.7388 (ptt) cc_final: 0.7162 (ptt)
REVERT: B   82 LYS cc_start: 0.8523 (tptt) cc_final: 0.7910 (tptp)
REVERT: B  436 ILE cc_start: 0.8816 (pt) cc_final: 0.8259 (mp)
REVERT: C   37 LEU cc_start: 0.9603 (mt) cc_final: 0.9315 (mp)
REVERT: C  181 TYR cc_start: 0.8096 (t80) cc_final: 0.7760 (t80)
REVERT: C  223 ILE cc_start: 0.8842 (tt) cc_final: 0.8634 (mp)
REVERT: C  440 MET cc_start: 0.8440 (tpt) cc_final: 0.8164 (tpp)
REVERT: D   12 ASP cc_start: 0.9200 (m-30) cc_final: 0.8995 (m-30)
REVERT: D   15 TYR cc_start: 0.8880 (t80) cc_final: 0.8670 (t80)
REVERT: D   55 VAL cc_start: 0.9013 (p) cc_final: 0.8744 (m)
REVERT: D   79 ARG cc_start: 0.9142 (mmt90) cc_final: 0.8584 (mmm-85)
REVERT: F    8 ASN cc_start: 0.9529 (m-40) cc_final: 0.9295 (m-40)
REVERT: F  104 TYR cc_start: 0.7844 (t80) cc_final: 0.7635 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 185
  average time/residue: 0.3148
  time to fit residues: 93.3300
Evaluate side-chains
  123 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 2.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 169 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 161 optimal weight:    9.9990
   chunk 187 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 235 optimal weight:    7.9990
   chunk 214 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  57 GLN
A 402 GLN
** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 GLN
C 102 ASN
C 244 HIS
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  43 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.078028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.056173 restraints weight = 111539.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.057630 restraints weight = 65571.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.058591 restraints weight = 46546.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.5841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  20780  Z= 0.207
  Angle     :  0.734   9.560  28106  Z= 0.389
  Chirality :  0.046   0.282   3114
  Planarity :  0.005   0.084   3646
  Dihedral  :  6.112  35.269   2730
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.31 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.94 (0.17), residues: 2502
  helix:  0.29 (0.15), residues: 1155
  sheet: -1.98 (0.33), residues: 227
  loop : -2.94 (0.17), residues: 1120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.003   TRP E 117 
 HIS   0.007   0.002   HIS B 244 
 PHE   0.020   0.002   PHE A 318 
 TYR   0.041   0.002   TYR A  30 
 ARG   0.006   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  825)
  hydrogen bonds       : angle       4.79309 ( 2352)
  covalent geometry    : bond        0.00441 (20780)
  covalent geometry    : angle       0.73369 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 2.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  117 TRP cc_start: 0.7543 (m-90) cc_final: 0.7222 (m-90)
REVERT: E  314 MET cc_start: 0.8060 (tpt) cc_final: 0.7725 (mmm)
REVERT: A  309 THR cc_start: 0.7744 (m) cc_final: 0.7449 (t)
REVERT: A  344 TYR cc_start: 0.9030 (t80) cc_final: 0.8649 (t80)
REVERT: A  390 MET cc_start: 0.9087 (ttm) cc_final: 0.8780 (ttm)
REVERT: A  604 MET cc_start: 0.7842 (pmm) cc_final: 0.7602 (pmm)
REVERT: A  658 MET cc_start: 0.8645 (mmt) cc_final: 0.8379 (mpp)
REVERT: A  683 MET cc_start: 0.8044 (ptt) cc_final: 0.7819 (ptt)
REVERT: A  994 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7602 (tt0)
REVERT: B  141 ASN cc_start: 0.7901 (t0) cc_final: 0.7649 (t0)
REVERT: C  223 ILE cc_start: 0.9142 (tt) cc_final: 0.8804 (mp)
REVERT: C  440 MET cc_start: 0.9018 (tpt) cc_final: 0.8788 (tpp)
REVERT: D   39 MET cc_start: 0.8901 (ttt) cc_final: 0.8601 (mmm)
REVERT: D   55 VAL cc_start: 0.9254 (p) cc_final: 0.9002 (m)
REVERT: D   79 ARG cc_start: 0.9245 (mmt90) cc_final: 0.8691 (mmm-85)
REVERT: F    6 THR cc_start: 0.8778 (t) cc_final: 0.8525 (t)
REVERT: F   15 TYR cc_start: 0.8813 (t80) cc_final: 0.8580 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2989
  time to fit residues: 74.1779
Evaluate side-chains
  105 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 2.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 209 optimal weight:    3.9990
   chunk 8 optimal weight:   30.0000
   chunk 164 optimal weight:    0.8980
   chunk 188 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 193 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 HIS
** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  21 ASN
C 102 ASN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  43 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.078800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.057011 restraints weight = 110359.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.058516 restraints weight = 64237.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.059529 restraints weight = 45512.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.6236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  20780  Z= 0.153
  Angle     :  0.657   8.168  28106  Z= 0.346
  Chirality :  0.045   0.186   3114
  Planarity :  0.004   0.080   3646
  Dihedral  :  5.818  33.072   2730
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -1.71 (0.17), residues: 2502
  helix:  0.58 (0.16), residues: 1132
  sheet: -2.08 (0.31), residues: 260
  loop : -2.82 (0.17), residues: 1110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP C  17 
 HIS   0.006   0.001   HIS E 313 
 PHE   0.017   0.001   PHE B 277 
 TYR   0.027   0.001   TYR A  30 
 ARG   0.004   0.000   ARG A 989 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  825)
  hydrogen bonds       : angle       4.57084 ( 2352)
  covalent geometry    : bond        0.00328 (20780)
  covalent geometry    : angle       0.65717 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 2.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  181 MET cc_start: 0.9063 (ptm) cc_final: 0.8780 (ppp)
REVERT: E  314 MET cc_start: 0.7968 (tpt) cc_final: 0.7645 (mmm)
REVERT: A  344 TYR cc_start: 0.8994 (t80) cc_final: 0.8625 (t80)
REVERT: A  390 MET cc_start: 0.9049 (ttm) cc_final: 0.8773 (ttm)
REVERT: A  589 ASN cc_start: 0.7239 (p0) cc_final: 0.6928 (p0)
REVERT: A  604 MET cc_start: 0.7927 (pmm) cc_final: 0.7631 (pmm)
REVERT: A  658 MET cc_start: 0.8573 (mmt) cc_final: 0.8268 (mpp)
REVERT: A  994 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7530 (tt0)
REVERT: B   87 TYR cc_start: 0.8744 (t80) cc_final: 0.8515 (t80)
REVERT: C  223 ILE cc_start: 0.9095 (tt) cc_final: 0.8802 (mp)
REVERT: C  275 ASP cc_start: 0.8252 (p0) cc_final: 0.7791 (p0)
REVERT: D   15 TYR cc_start: 0.9008 (t80) cc_final: 0.8709 (t80)
REVERT: D   17 MET cc_start: 0.8380 (ttm) cc_final: 0.8155 (ttm)
REVERT: D   55 VAL cc_start: 0.9269 (p) cc_final: 0.8986 (m)
REVERT: D   79 ARG cc_start: 0.9231 (mmt90) cc_final: 0.8728 (mmm-85)
REVERT: D   81 LEU cc_start: 0.9461 (mt) cc_final: 0.9243 (pp)
REVERT: F   15 TYR cc_start: 0.8827 (t80) cc_final: 0.8447 (t80)
REVERT: F   89 LEU cc_start: 0.9454 (mm) cc_final: 0.9225 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2924
  time to fit residues: 73.5387
Evaluate side-chains
  103 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 2.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 191 optimal weight:    9.9990
   chunk 144 optimal weight:    4.9990
   chunk 183 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 221 optimal weight:    2.9990
   chunk 154 optimal weight:    6.9990
   chunk 215 optimal weight:    2.9990
   chunk 229 optimal weight:    3.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 ASN
B 289 HIS
B 345 ASN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 ASN
C 217 GLN
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  43 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.076688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054692 restraints weight = 113552.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056129 restraints weight = 66586.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.057081 restraints weight = 47564.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.7026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  20780  Z= 0.221
  Angle     :  0.732   9.131  28106  Z= 0.388
  Chirality :  0.047   0.191   3114
  Planarity :  0.005   0.059   3646
  Dihedral  :  6.124  34.125   2730
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.96 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.81 (0.17), residues: 2502
  helix:  0.45 (0.16), residues: 1143
  sheet: -2.04 (0.31), residues: 266
  loop : -2.86 (0.18), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP C  17 
 HIS   0.007   0.002   HIS E 313 
 PHE   0.055   0.002   PHE B 277 
 TYR   0.034   0.002   TYR F  15 
 ARG   0.005   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  825)
  hydrogen bonds       : angle       4.76560 ( 2352)
  covalent geometry    : bond        0.00471 (20780)
  covalent geometry    : angle       0.73208 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 2.351 
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: E  181 MET cc_start: 0.9013 (ptm) cc_final: 0.8723 (ppp)
REVERT: E  203 TRP cc_start: 0.7865 (m-10) cc_final: 0.7550 (m100)
REVERT: A  309 THR cc_start: 0.7807 (m) cc_final: 0.7554 (t)
REVERT: A  344 TYR cc_start: 0.9005 (t80) cc_final: 0.8525 (t80)
REVERT: A  390 MET cc_start: 0.9054 (ttm) cc_final: 0.8801 (ttm)
REVERT: A  589 ASN cc_start: 0.7726 (p0) cc_final: 0.7208 (p0)
REVERT: A  604 MET cc_start: 0.8004 (pmm) cc_final: 0.7509 (pmm)
REVERT: A  994 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7619 (tt0)
REVERT: B  141 ASN cc_start: 0.6721 (t0) cc_final: 0.6412 (m-40)
REVERT: C  136 PHE cc_start: 0.7367 (p90) cc_final: 0.6639 (p90)
REVERT: C  223 ILE cc_start: 0.9235 (tt) cc_final: 0.8953 (mp)
REVERT: C  265 MET cc_start: 0.9462 (mtt) cc_final: 0.9015 (mtt)
REVERT: D   17 MET cc_start: 0.8346 (ttm) cc_final: 0.8140 (ttm)
REVERT: D   79 ARG cc_start: 0.9286 (mmt90) cc_final: 0.8811 (mmm-85)
REVERT: D   88 GLN cc_start: 0.9419 (tp40) cc_final: 0.9148 (tp-100)
REVERT: F   61 ILE cc_start: 0.8489 (mt) cc_final: 0.7787 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2911
  time to fit residues: 69.1701
Evaluate side-chains
  100 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 2.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 195 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 241 optimal weight:    9.9990
   chunk 140 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 169 optimal weight:    5.9990
   chunk 148 optimal weight:    0.0670
   chunk 204 optimal weight:    0.0570
   chunk 98 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 142 optimal weight:    4.9990
   overall best weight:    1.6240

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

Flipped N/Q/H residues before XYZ refinement:
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 HIS
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
B 373 GLN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 ASN
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.078192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.056068 restraints weight = 112425.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.057553 restraints weight = 65667.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.058542 restraints weight = 46925.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.7196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20780  Z= 0.143
  Angle     :  0.668   8.359  28106  Z= 0.351
  Chirality :  0.045   0.185   3114
  Planarity :  0.004   0.062   3646
  Dihedral  :  5.798  31.995   2730
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -1.61 (0.17), residues: 2502
  helix:  0.64 (0.16), residues: 1140
  sheet: -2.14 (0.30), residues: 274
  loop : -2.73 (0.18), residues: 1088

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP E 117 
 HIS   0.011   0.001   HIS E 313 
 PHE   0.034   0.001   PHE B 277 
 TYR   0.025   0.001   TYR E 310 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  825)
  hydrogen bonds       : angle       4.59666 ( 2352)
  covalent geometry    : bond        0.00308 (20780)
  covalent geometry    : angle       0.66752 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 3.385 
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: E  117 TRP cc_start: 0.7303 (m-90) cc_final: 0.7089 (m-90)
REVERT: E  181 MET cc_start: 0.9010 (ptm) cc_final: 0.8722 (ppp)
REVERT: E  203 TRP cc_start: 0.7888 (m-10) cc_final: 0.7537 (m100)
REVERT: A  309 THR cc_start: 0.7690 (m) cc_final: 0.7422 (t)
REVERT: A  344 TYR cc_start: 0.9003 (t80) cc_final: 0.8752 (t80)
REVERT: A  390 MET cc_start: 0.9015 (ttm) cc_final: 0.8778 (ttm)
REVERT: A  511 MET cc_start: 0.8151 (tpp) cc_final: 0.7944 (tpp)
REVERT: A  589 ASN cc_start: 0.7624 (p0) cc_final: 0.7236 (p0)
REVERT: A  604 MET cc_start: 0.8014 (pmm) cc_final: 0.7548 (pmm)
REVERT: A  910 MET cc_start: 0.7806 (mmp) cc_final: 0.6645 (mmm)
REVERT: B  181 TYR cc_start: 0.8871 (t80) cc_final: 0.8047 (t80)
REVERT: B  262 LEU cc_start: 0.9653 (pp) cc_final: 0.9420 (tp)
REVERT: B  267 MET cc_start: 0.7952 (tmm) cc_final: 0.7716 (tmm)
REVERT: B  436 ILE cc_start: 0.9074 (pt) cc_final: 0.8504 (mp)
REVERT: C  136 PHE cc_start: 0.7466 (p90) cc_final: 0.6850 (p90)
REVERT: C  223 ILE cc_start: 0.9052 (tt) cc_final: 0.8785 (mp)
REVERT: C  265 MET cc_start: 0.9471 (mtt) cc_final: 0.8998 (mtt)
REVERT: D   39 MET cc_start: 0.8923 (ttt) cc_final: 0.8624 (mmm)
REVERT: D   79 ARG cc_start: 0.9272 (mmt90) cc_final: 0.8819 (mmm-85)
REVERT: D   88 GLN cc_start: 0.9554 (tp40) cc_final: 0.9116 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.3784
  time to fit residues: 87.9945
Evaluate side-chains
  97 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 3.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 152 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 134 optimal weight:    3.9990
   chunk 124 optimal weight:   30.0000
   chunk 135 optimal weight:    0.6980
   chunk 157 optimal weight:    2.9990
   chunk 176 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9990
   chunk 149 optimal weight:    0.8980
   chunk 141 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 635 GLN
B 345 ASN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 ASN
B 428 ASN
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN
C 102 ASN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.079106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.057310 restraints weight = 110322.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.058831 restraints weight = 64425.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.059835 restraints weight = 45709.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.7381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  20780  Z= 0.119
  Angle     :  0.646   8.199  28106  Z= 0.337
  Chirality :  0.044   0.189   3114
  Planarity :  0.004   0.057   3646
  Dihedral  :  5.534  32.399   2730
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -1.39 (0.17), residues: 2502
  helix:  0.83 (0.16), residues: 1127
  sheet: -2.04 (0.31), residues: 268
  loop : -2.58 (0.18), residues: 1107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP C  17 
 HIS   0.010   0.001   HIS E 313 
 PHE   0.024   0.001   PHE C 268 
 TYR   0.031   0.001   TYR E 310 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  825)
  hydrogen bonds       : angle       4.48912 ( 2352)
  covalent geometry    : bond        0.00255 (20780)
  covalent geometry    : angle       0.64597 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 3.498 
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: E  117 TRP cc_start: 0.7189 (m-10) cc_final: 0.6980 (m-90)
REVERT: E  181 MET cc_start: 0.9036 (ptm) cc_final: 0.8803 (ppp)
REVERT: E  203 TRP cc_start: 0.7830 (m-10) cc_final: 0.7322 (m100)
REVERT: A  390 MET cc_start: 0.9069 (ttm) cc_final: 0.8822 (ttm)
REVERT: A  511 MET cc_start: 0.8183 (tpp) cc_final: 0.7978 (tpp)
REVERT: A  589 ASN cc_start: 0.7640 (p0) cc_final: 0.7245 (p0)
REVERT: A  604 MET cc_start: 0.8082 (pmm) cc_final: 0.7649 (pmm)
REVERT: A  658 MET cc_start: 0.8735 (mmt) cc_final: 0.8313 (mpp)
REVERT: B  181 TYR cc_start: 0.8962 (t80) cc_final: 0.8548 (t80)
REVERT: B  265 MET cc_start: 0.9290 (ttm) cc_final: 0.9038 (ttm)
REVERT: B  267 MET cc_start: 0.8052 (tmm) cc_final: 0.7813 (tmm)
REVERT: B  436 ILE cc_start: 0.9131 (pt) cc_final: 0.8534 (mp)
REVERT: C  136 PHE cc_start: 0.7406 (p90) cc_final: 0.6852 (p90)
REVERT: C  223 ILE cc_start: 0.8919 (tt) cc_final: 0.8687 (mp)
REVERT: D   17 MET cc_start: 0.8426 (ttm) cc_final: 0.8190 (ttm)
REVERT: D   39 MET cc_start: 0.8943 (ttt) cc_final: 0.8597 (mmm)
REVERT: D   79 ARG cc_start: 0.9228 (mmt90) cc_final: 0.8797 (mmm-85)
REVERT: D   88 GLN cc_start: 0.9545 (tp40) cc_final: 0.8959 (tp-100)
REVERT: F   89 LEU cc_start: 0.9414 (mm) cc_final: 0.9129 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.4315
  time to fit residues: 108.2348
Evaluate side-chains
  102 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 4.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 215 optimal weight:    0.8980
   chunk 219 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 141 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 156 optimal weight:    0.6980
   chunk 151 optimal weight:    7.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN
C 102 ASN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.078320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.056853 restraints weight = 111575.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.058705 restraints weight = 71353.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.059046 restraints weight = 43087.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.7594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20780  Z= 0.145
  Angle     :  0.659   9.148  28106  Z= 0.343
  Chirality :  0.044   0.216   3114
  Planarity :  0.004   0.057   3646
  Dihedral  :  5.529  32.422   2730
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -1.38 (0.17), residues: 2502
  helix:  0.77 (0.16), residues: 1142
  sheet: -1.92 (0.32), residues: 257
  loop : -2.58 (0.18), residues: 1103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP C  17 
 HIS   0.008   0.001   HIS E 313 
 PHE   0.028   0.001   PHE C 362 
 TYR   0.024   0.001   TYR E 310 
 ARG   0.004   0.000   ARG B 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  825)
  hydrogen bonds       : angle       4.48030 ( 2352)
  covalent geometry    : bond        0.00313 (20780)
  covalent geometry    : angle       0.65854 (28106)

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

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

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5004 Ramachandran restraints generated.
    2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 4.248 
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: E  181 MET cc_start: 0.9074 (ptm) cc_final: 0.8854 (ppp)
REVERT: A  309 THR cc_start: 0.7787 (m) cc_final: 0.7566 (t)
REVERT: A  347 MET cc_start: 0.8660 (tmm) cc_final: 0.8429 (ppp)
REVERT: A  390 MET cc_start: 0.9120 (ttm) cc_final: 0.8846 (ttm)
REVERT: A  511 MET cc_start: 0.8073 (tpp) cc_final: 0.7862 (tpp)
REVERT: A  604 MET cc_start: 0.8120 (pmm) cc_final: 0.7678 (pmm)
REVERT: A  658 MET cc_start: 0.8554 (mmt) cc_final: 0.8297 (mpp)
REVERT: B  181 TYR cc_start: 0.8959 (t80) cc_final: 0.8503 (t80)
REVERT: B  267 MET cc_start: 0.7764 (tmm) cc_final: 0.7454 (tmm)
REVERT: B  436 ILE cc_start: 0.9175 (pt) cc_final: 0.8606 (mp)
REVERT: C  136 PHE cc_start: 0.7589 (p90) cc_final: 0.6968 (p90)
REVERT: C  223 ILE cc_start: 0.9017 (tt) cc_final: 0.8772 (mp)
REVERT: C  265 MET cc_start: 0.9405 (mtm) cc_final: 0.8897 (mtt)
REVERT: C  275 ASP cc_start: 0.7704 (p0) cc_final: 0.7207 (p0)
REVERT: D   39 MET cc_start: 0.8945 (ttt) cc_final: 0.8571 (mmm)
REVERT: D   56 MET cc_start: 0.9261 (tpt) cc_final: 0.8509 (tpp)
REVERT: D   79 ARG cc_start: 0.9221 (mmt90) cc_final: 0.8879 (mmt90)
REVERT: D   88 GLN cc_start: 0.9557 (tp40) cc_final: 0.9245 (tp40)
REVERT: F   82 GLN cc_start: 0.9526 (mt0) cc_final: 0.9325 (mt0)
REVERT: F   89 LEU cc_start: 0.9431 (mm) cc_final: 0.9138 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.4939
  time to fit residues: 117.7805
Evaluate side-chains
  102 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 3.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 250 optimal weight:    5.9990
   chunk 211 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 177 optimal weight:    5.9990
   chunk 145 optimal weight:    4.9990
   chunk 151 optimal weight:    8.9990
   chunk 185 optimal weight:    0.0870
   chunk 23 optimal weight:    0.5980
   chunk 136 optimal weight:    2.9990
   chunk 184 optimal weight:    4.9990
   overall best weight:    1.7364

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

Flipped N/Q/H residues before XYZ refinement:
** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN
C 102 ASN
** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.078278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.056379 restraints weight = 112717.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.057862 restraints weight = 65477.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.058852 restraints weight = 46434.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.7823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  20780  Z= 0.145
  Angle     :  0.656   8.805  28106  Z= 0.342
  Chirality :  0.044   0.205   3114
  Planarity :  0.004   0.057   3646
  Dihedral  :  5.495  32.332   2730
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 2.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -1.34 (0.17), residues: 2502
  helix:  0.84 (0.16), residues: 1140
  sheet: -2.05 (0.30), residues: 271
  loop : -2.54 (0.18), residues: 1091

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C  17 
 HIS   0.009   0.001   HIS E 313 
 PHE   0.025   0.002   PHE B 199 
 TYR   0.026   0.001   TYR E 310 
 ARG   0.004   0.000   ARG B 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  825)
  hydrogen bonds       : angle       4.49021 ( 2352)
  covalent geometry    : bond        0.00314 (20780)
  covalent geometry    : angle       0.65608 (28106)

===============================================================================
Job complete
usr+sys time: 7281.36 seconds
wall clock time: 131 minutes 55.57 seconds (7915.57 seconds total)