Starting phenix.real_space_refine
on Sat Aug 23 05:21:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uic_42292/08_2025/8uic_42292.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.109
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      77      5.16       5
     C    6436      2.51       5
     N    1658      2.21       5
     O    1798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9971
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "K"
      Number of atoms: 3340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3340
          Classifications: {'peptide': 424}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 403}
          Chain breaks: 3
    Chain: "T"
      Number of atoms: 6629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 803, 6629
          Classifications: {'peptide': 803}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 788}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9956  SG  CYS T 973      31.553  58.803  51.985  1.00 62.13           S
  ATOM   9956  SG  CYS T 973      31.553  58.803  51.985  1.00 62.13           S

  Time building chain proxies: 2.82, per 1000 atoms: 0.28
  Number of scatterers: 9971
  At special positions: 0
  Unit cell: (95.304, 95.304, 112.632, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      77     16.00
     O    1798      8.00
     N    1658      7.00
     C    6436      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 408.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 800 "
        pdb="ZN    ZN K 800 " - pdb=" ND1 HIS K  70 "
        pdb="ZN    ZN K 800 " - pdb=" NE2 HIS K 157 "
        pdb="ZN    ZN K 800 " - pdb=" NE2 HIS K  68 "
        pdb="ZN    ZN K 800 " - pdb=" SG  CYS T 973 "
      pdb="  ZN K 801 "
        pdb="ZN    ZN K 801 " - pdb=" SG  CYS T 973 "
        pdb="ZN    ZN K 801 " - pdb=" NE2 HIS K  73 "
        pdb="ZN    ZN K 801 " - pdb=" NE2 HIS K 414 "
      Number of angles added : 3


  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 6 sheets defined
      65.3% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'K' and resid 41 through 45
      removed outlier: 3.837A  pdb=" N   PHE K  45 " --> pdb=" O   GLU K  42 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 76 through 83
    Processing helix  chain 'K' and resid 94 through 112
      Proline residue:  K 101  - end of helix
    Processing helix  chain 'K' and resid 122 through 132
      removed outlier: 4.031A  pdb=" N   LYS K 132 " --> pdb=" O   ASP K 128 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 216 through 230
      removed outlier: 3.965A  pdb=" N   ASP K 220 " --> pdb=" O   CYS K 216 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE K 221 " --> pdb=" O   ARG K 217 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS K 224 " --> pdb=" O   ASP K 220 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU K 227 " --> pdb=" O   LYS K 223 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 244 through 249
      removed outlier: 3.664A  pdb=" N   LEU K 248 " --> pdb=" O   ARG K 244 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   CYS K 249 " --> pdb=" O   ALA K 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 244 through 249'
    Processing helix  chain 'K' and resid 250 through 259
    Processing helix  chain 'K' and resid 273 through 286
      removed outlier: 3.884A  pdb=" N   TYR K 279 " --> pdb=" O   ALA K 275 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE K 283 " --> pdb=" O   TYR K 279 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR K 284 " --> pdb=" O   LYS K 280 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 309 through 315
      removed outlier: 3.663A  pdb=" N   ILE K 313 " --> pdb=" O   LYS K 310 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP K 314 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 331 through 341
      removed outlier: 3.594A  pdb=" N   GLN K 335 " --> pdb=" O   GLY K 331 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS K 339 " --> pdb=" O   GLN K 335 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 358 through 365
      removed outlier: 3.774A  pdb=" N   LYS K 362 " --> pdb=" O   THR K 358 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 394 through 406
      removed outlier: 3.637A  pdb=" N   ILE K 398 " --> pdb=" O   ASP K 394 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   MET K 399 " --> pdb=" O   ALA K 395 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 416 through 432
      removed outlier: 3.702A  pdb=" N   SER K 425 " --> pdb=" O   LYS K 421 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS K 426 " --> pdb=" O   PHE K 422 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 3 through 19
      removed outlier: 3.532A  pdb=" N   LEU T  19 " --> pdb=" O   PHE T  15 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 28 through 40
      removed outlier: 3.650A  pdb=" N   GLU T  32 " --> pdb=" O   ASN T  28 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 41 through 43
      No H-bonds generated for 'chain 'T' and resid 41 through 43'
    Processing helix  chain 'T' and resid 44 through 49
      removed outlier: 3.694A  pdb=" N   GLN T  48 " --> pdb=" O   ALA T  44 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 51 through 64
    Processing helix  chain 'T' and resid 73 through 86
      removed outlier: 3.729A  pdb=" N   PHE T  77 " --> pdb=" O   LYS T  73 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 90 through 98
      removed outlier: 3.529A  pdb=" N   ARG T  94 " --> pdb=" O   TRP T  90 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 99 through 111
    Processing helix  chain 'T' and resid 117 through 131
      removed outlier: 3.879A  pdb=" N   VAL T 131 " --> pdb=" O   LYS T 127 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 132 through 143
    Processing helix  chain 'T' and resid 144 through 155
      removed outlier: 3.609A  pdb=" N   LEU T 148 " --> pdb=" O   ILE T 144 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 160 through 178
      removed outlier: 4.572A  pdb=" N   GLN T 166 " --> pdb=" O   ARG T 162 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL T 167 " --> pdb=" O   GLU T 163 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 181 through 200
      removed outlier: 4.038A  pdb=" N   THR T 185 " --> pdb=" O   ASP T 181 " (cutoff:3.500A)
      Proline residue:  T 195  - end of helix
      removed outlier: 3.784A  pdb=" N   ASN T 199 " --> pdb=" O   PRO T 195 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 218 through 240
      removed outlier: 3.849A  pdb=" N   LYS T 222 " --> pdb=" O   GLU T 218 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU T 240 " --> pdb=" O   GLN T 236 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 245 through 253
    Processing helix  chain 'T' and resid 255 through 267
      removed outlier: 3.582A  pdb=" N   THR T 259 " --> pdb=" O   ASP T 255 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ASP T 265 " --> pdb=" O   TRP T 261 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   MET T 266 " --> pdb=" O   LYS T 262 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR T 267 " --> pdb=" O   LEU T 263 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 269 through 293
      removed outlier: 3.827A  pdb=" N   GLU T 274 " --> pdb=" O   PRO T 270 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LYS T 275 " --> pdb=" O   TYR T 271 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE T 276 " --> pdb=" O   PHE T 272 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 305 through 323
      removed outlier: 3.939A  pdb=" N   ALA T 311 " --> pdb=" O   GLU T 307 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS T 323 " --> pdb=" O   LEU T 319 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 325 through 343
      removed outlier: 3.896A  pdb=" N   GLY T 343 " --> pdb=" O   TRP T 339 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 358 through 377
      removed outlier: 4.297A  pdb=" N   GLN T 362 " --> pdb=" O   THR T 358 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU T 363 " --> pdb=" O   PHE T 359 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE T 364 " --> pdb=" O   GLU T 360 " (cutoff:3.500A)
      Proline residue:  T 370  - end of helix
      removed outlier: 3.683A  pdb=" N   TYR T 377 " --> pdb=" O   PHE T 373 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 394 through 399
      removed outlier: 3.542A  pdb=" N   LEU T 398 " --> pdb=" O   TYR T 394 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 400 through 402
      No H-bonds generated for 'chain 'T' and resid 400 through 402'
    Processing helix  chain 'T' and resid 403 through 417
      removed outlier: 3.677A  pdb=" N   LEU T 409 " --> pdb=" O   GLN T 405 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ASP T 415 " --> pdb=" O   TYR T 411 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 432 through 443
    Processing helix  chain 'T' and resid 444 through 446
      No H-bonds generated for 'chain 'T' and resid 444 through 446'
    Processing helix  chain 'T' and resid 449 through 468
      removed outlier: 3.727A  pdb=" N   VAL T 453 " --> pdb=" O   ARG T 449 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 505 through 523
    Processing helix  chain 'T' and resid 531 through 546
      removed outlier: 4.462A  pdb=" N   THR T 546 " --> pdb=" O   VAL T 542 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 549 through 567
      removed outlier: 3.716A  pdb=" N   THR T 553 " --> pdb=" O   ASP T 549 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL T 554 " --> pdb=" O   ALA T 550 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLN T 555 " --> pdb=" O   ARG T 551 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 583 through 595
      Proline residue:  T 589  - end of helix
      removed outlier: 3.842A  pdb=" N   VAL T 592 " --> pdb=" O   GLY T 588 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 599 through 617
      removed outlier: 3.625A  pdb=" N   ARG T 603 " --> pdb=" O   MET T 599 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR T 605 " --> pdb=" O   GLU T 601 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 625 through 630
    Processing helix  chain 'T' and resid 632 through 643
      removed outlier: 3.694A  pdb=" N   ILE T 636 " --> pdb=" O   LYS T 632 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ASN T 643 " --> pdb=" O   GLU T 639 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 646 through 660
    Processing helix  chain 'T' and resid 663 through 670
    Processing helix  chain 'T' and resid 675 through 686
      removed outlier: 4.329A  pdb=" N   HIS T 679 " --> pdb=" O   ASP T 675 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR T 685 " --> pdb=" O   LEU T 681 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 690 through 707
      removed outlier: 3.787A  pdb=" N   SER T 694 " --> pdb=" O   ASP T 690 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU T 695 " --> pdb=" O   ILE T 691 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 710 through 712
      No H-bonds generated for 'chain 'T' and resid 710 through 712'
    Processing helix  chain 'T' and resid 713 through 724
    Processing helix  chain 'T' and resid 730 through 750
      removed outlier: 3.516A  pdb=" N   LYS T 734 " --> pdb=" O   HIS T 730 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER T 750 " --> pdb=" O   TYR T 746 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 777 through 794
      removed outlier: 3.909A  pdb=" N   TYR T 793 " --> pdb=" O   GLU T 789 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 795 through 806
      removed outlier: 3.638A  pdb=" N   GLU T 805 " --> pdb=" O   LYS T 801 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 809 through 823
      removed outlier: 3.727A  pdb=" N   GLU T 813 " --> pdb=" O   MET T 809 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 873 through 880
    Processing helix  chain 'T' and resid 888 through 894
    Processing helix  chain 'T' and resid 913 through 919
      removed outlier: 3.985A  pdb=" N   GLN T 917 " --> pdb=" O   TYR T 914 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA T 919 " --> pdb=" O   LYS T 916 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 921 through 932
      removed outlier: 3.582A  pdb=" N   GLU T 927 " --> pdb=" O   ARG T 923 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU T 929 " --> pdb=" O   PHE T 925 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ILE T 932 " --> pdb=" O   GLU T 928 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 934 through 949
      removed outlier: 4.019A  pdb=" N   VAL T 938 " --> pdb=" O   LEU T 934 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   HIS T 941 " --> pdb=" O   LEU T 937 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLN T 942 " --> pdb=" O   VAL T 938 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE T 945 " --> pdb=" O   HIS T 941 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLU T 949 " --> pdb=" O   PHE T 945 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 950 through 964
    Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 6
      removed outlier: 3.771A  pdb=" N   ILE K   6 " --> pdb=" O   CYS K 444 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 64 through 65
      removed outlier: 6.505A  pdb=" N   VAL K  64 " --> pdb=" O   TYR K  91 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   THR K  93 " --> pdb=" O   VAL K  64 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ILE K  90 " --> pdb=" O   ILE K 134 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL K 136 " --> pdb=" O   ILE K  90 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   MET K  92 " --> pdb=" O   VAL K 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'K' and resid 142 through 144
      removed outlier: 4.121A  pdb=" N   LEU K 148 " --> pdb=" O   VAL K 144 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ILE K 201 " --> pdb=" O   SER K 172 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL K 174 " --> pdb=" O   ILE K 201 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   GLU K 203 " --> pdb=" O   VAL K 174 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   LEU K 412 " --> pdb=" O   LEU K 200 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   SER K 202 " --> pdb=" O   LEU K 412 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   HIS K 414 " --> pdb=" O   SER K 202 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 320 through 323
      removed outlier: 4.162A  pdb=" N   VAL K 348 " --> pdb=" O   ALA K 383 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU K 385 " --> pdb=" O   VAL K 348 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   MET K 350 " --> pdb=" O   GLU K 385 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 265 through 266
      removed outlier: 6.059A  pdb=" N   ILE K 265 " --> pdb=" O   LYS K 306 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'K' and resid 370 through 371
      removed outlier: 3.604A  pdb=" N   VAL K 370 " --> pdb=" O   VAL K 378 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1452 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: 1.71

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1621
        1.30 -     1.42: 2577
        1.42 -     1.55: 5846
        1.55 -     1.68: 0
        1.68 -     1.81: 127
  Bond restraints: 10171
  Sorted by residual:
  bond pdb=" C   VAL K 348 "
       pdb=" O   VAL K 348 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.19e-02 7.06e+03 3.40e+01
  bond pdb=" CA  ALA K 318 "
       pdb=" CB  ALA K 318 "
    ideal  model  delta    sigma   weight residual
    1.529  1.471  0.057 1.66e-02 3.63e+03 1.19e+01
  bond pdb=" N   PRO K 351 "
       pdb=" CA  PRO K 351 "
    ideal  model  delta    sigma   weight residual
    1.469  1.426  0.043 1.28e-02 6.10e+03 1.13e+01
  bond pdb=" C   PRO K 351 "
       pdb=" O   PRO K 351 "
    ideal  model  delta    sigma   weight residual
    1.235  1.192  0.043 1.30e-02 5.92e+03 1.10e+01
  bond pdb=" C   ILE K 349 "
       pdb=" O   ILE K 349 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.037 1.19e-02 7.06e+03 9.74e+00
  ... (remaining 10166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 13051
        2.00 -     4.00: 527
        4.00 -     6.00: 115
        6.00 -     7.99: 31
        7.99 -     9.99: 6
  Bond angle restraints: 13730
  Sorted by residual:
  angle pdb=" N   PRO K 316 "
        pdb=" CA  PRO K 316 "
        pdb=" C   PRO K 316 "
      ideal   model   delta    sigma   weight residual
     113.53  122.97   -9.44 1.39e+00 5.18e-01 4.62e+01
  angle pdb=" C   ASN K 315 "
        pdb=" CA  ASN K 315 "
        pdb=" CB  ASN K 315 "
      ideal   model   delta    sigma   weight residual
     109.42  119.41   -9.99 1.57e+00 4.06e-01 4.05e+01
  angle pdb=" CA  MET K 319 "
        pdb=" C   MET K 319 "
        pdb=" O   MET K 319 "
      ideal   model   delta    sigma   weight residual
     121.45  115.06    6.39 1.07e+00 8.73e-01 3.57e+01
  angle pdb=" N   LYS K 381 "
        pdb=" CA  LYS K 381 "
        pdb=" C   LYS K 381 "
      ideal   model   delta    sigma   weight residual
     113.89  104.71    9.18 1.58e+00 4.01e-01 3.38e+01
  angle pdb=" N   LEU K 364 "
        pdb=" CA  LEU K 364 "
        pdb=" C   LEU K 364 "
      ideal   model   delta    sigma   weight residual
     113.18  106.56    6.62 1.21e+00 6.83e-01 2.99e+01
  ... (remaining 13725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 5293
       17.13 -    34.26: 662
       34.26 -    51.39: 127
       51.39 -    68.52: 30
       68.52 -    85.65: 15
  Dihedral angle restraints: 6127
    sinusoidal: 2513
      harmonic: 3614
  Sorted by residual:
  dihedral pdb=" CA  VAL K 144 "
           pdb=" C   VAL K 144 "
           pdb=" N   ASP K 145 "
           pdb=" CA  ASP K 145 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  LEU T 447 "
           pdb=" C   LEU T 447 "
           pdb=" N   ASP T 448 "
           pdb=" CA  ASP T 448 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.73  -26.27     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ASP T 255 "
           pdb=" C   ASP T 255 "
           pdb=" N   PHE T 256 "
           pdb=" CA  PHE T 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.32  -25.68     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 6124 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1298
       0.071 -    0.141: 225
       0.141 -    0.212: 35
       0.212 -    0.282: 8
       0.282 -    0.353: 4
  Chirality restraints: 1570
  Sorted by residual:
  chirality pdb=" CA  PRO K 316 "
            pdb=" N   PRO K 316 "
            pdb=" C   PRO K 316 "
            pdb=" CB  PRO K 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CB  THR K   7 "
            pdb=" CA  THR K   7 "
            pdb=" OG1 THR K   7 "
            pdb=" CG2 THR K   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.20    0.35 2.00e-01 2.50e+01 3.10e+00
  chirality pdb=" CA  VAL K 378 "
            pdb=" N   VAL K 378 "
            pdb=" C   VAL K 378 "
            pdb=" CB  VAL K 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.79   -0.35 2.00e-01 2.50e+01 2.98e+00
  ... (remaining 1567 not shown)

  Planarity restraints: 1712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE K 372 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.20e+01
        pdb=" C   PHE K 372 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   PHE K 372 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU K 373 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS K 310 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.28e+00
        pdb=" C   LYS K 310 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS K 310 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ALA K 311 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU K 385 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.97e+00
        pdb=" C   GLU K 385 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   GLU K 385 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYR K 386 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1709 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 126
        2.65 -     3.21: 9301
        3.21 -     3.77: 14814
        3.77 -     4.34: 19328
        4.34 -     4.90: 32657
  Nonbonded interactions: 76226
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP K 178 "
            pdb="ZN    ZN K 800 "
     model   vdw
     2.082 2.230
  nonbonded pdb=" OG1 THR K  96 "
            pdb=" O   GLY K 160 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD2 ASP K  72 "
            pdb="ZN    ZN K 801 "
     model   vdw
     2.224 2.230
  nonbonded pdb=" OH  TYR K 153 "
            pdb=" OD2 ASP K 193 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   GLU T 687 "
            pdb=" NH2 ARG T 693 "
     model   vdw
     2.261 3.120
  ... (remaining 76221 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
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   0.070  10178  Z= 0.341
  Angle     :  0.974   9.993  13733  Z= 0.562
  Chirality :  0.060   0.353   1570
  Planarity :  0.005   0.056   1712
  Dihedral  : 16.026  85.653   3771
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  0.90 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.23), residues: 1199
  helix: -0.27 (0.19), residues: 701
  sheet: -0.31 (0.81), residues: 49
  loop : -2.69 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG T 140 
 TYR   0.034   0.002   TYR K 179 
 PHE   0.033   0.003   PHE K 267 
 TRP   0.033   0.002   TRP K 256 
 HIS   0.008   0.001   HIS K  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00707 (10171)
  covalent geometry    : angle       0.97085 (13730)
  hydrogen bonds       : bond        0.14810 (  492)
  hydrogen bonds       : angle       6.12299 ( 1452)
  metal coordination   : bond        0.01601 (    7)
  metal coordination   : angle       5.01274 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: K   92 MET cc_start: 0.8138 (ptm) cc_final: 0.7860 (ptm)
REVERT: K  257 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7606 (tp30)
REVERT: K  280 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7749 (ttpp)
REVERT: K  343 ASN cc_start: 0.8512 (t0) cc_final: 0.8285 (t0)
REVERT: K  369 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8030 (mtpp)
REVERT: K  371 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7220 (mm-30)
REVERT: K  372 PHE cc_start: 0.8530 (m-80) cc_final: 0.8156 (m-80)
REVERT: K  375 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7102 (mmt90)
REVERT: T   39 GLN cc_start: 0.8214 (mm110) cc_final: 0.7994 (tp40)
REVERT: T  746 TYR cc_start: 0.8712 (m-80) cc_final: 0.8475 (m-10)
REVERT: T  822 MET cc_start: 0.8494 (ttp) cc_final: 0.8163 (ttp)
REVERT: T  957 ASP cc_start: 0.8306 (t0) cc_final: 0.8071 (t0)
  outliers start: 22
  outliers final: 4
  residues processed: 192
  average time/residue: 0.1000
  time to fit residues: 27.9816
Evaluate side-chains
  143 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  369 LYS
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  371 GLU
Chi-restraints excluded: chain K residue  375 ARG
Chi-restraints excluded: chain K residue  380 VAL
Chi-restraints excluded: chain K residue  382 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.5980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
K 374 ASN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 566 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.165785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.135195 restraints weight = 13348.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.139698 restraints weight = 7796.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.141160 restraints weight = 5415.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.141643 restraints weight = 4361.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142160 restraints weight = 4222.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10178  Z= 0.145
  Angle     :  0.616   9.847  13733  Z= 0.323
  Chirality :  0.042   0.248   1570
  Planarity :  0.004   0.056   1712
  Dihedral  :  6.625  58.520   1330
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  8.75 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.25), residues: 1199
  helix:  0.52 (0.20), residues: 712
  sheet: -0.67 (0.75), residues: 54
  loop : -2.51 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG T 140 
 TYR   0.012   0.001   TYR T 461 
 PHE   0.030   0.002   PHE K 267 
 TRP   0.012   0.001   TRP T 339 
 HIS   0.007   0.001   HIS K 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10171)
  covalent geometry    : angle       0.61391 (13730)
  hydrogen bonds       : bond        0.03826 (  492)
  hydrogen bonds       : angle       4.39704 ( 1452)
  metal coordination   : bond        0.01336 (    7)
  metal coordination   : angle       3.82120 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: K   92 MET cc_start: 0.8132 (ptm) cc_final: 0.7900 (ptm)
REVERT: K  280 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7833 (ttpp)
REVERT: T  319 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7506 (mm)
REVERT: T  449 ARG cc_start: 0.8729 (tpt90) cc_final: 0.8395 (tpt90)
REVERT: T  746 TYR cc_start: 0.8595 (m-80) cc_final: 0.8391 (m-10)
REVERT: T  822 MET cc_start: 0.8567 (ttp) cc_final: 0.8274 (ttt)
  outliers start: 27
  outliers final: 19
  residues processed: 159
  average time/residue: 0.0931
  time to fit residues: 21.8449
Evaluate side-chains
  149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  380 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  112 HIS
Chi-restraints excluded: chain T residue  144 ILE
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  319 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0270
   chunk 82 optimal weight:    3.9990
   overall best weight:    2.0222

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

Flipped N/Q/H residues before XYZ refinement:
K 329 HIS
T  28 ASN
T  39 GLN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** 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 = 0.3980 r_free = 0.3980 target = 0.161148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130433 restraints weight = 13537.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.134440 restraints weight = 8148.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.135744 restraints weight = 5773.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.136551 restraints weight = 4695.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.136813 restraints weight = 4437.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10178  Z= 0.211
  Angle     :  0.646   9.996  13733  Z= 0.339
  Chirality :  0.044   0.205   1570
  Planarity :  0.004   0.047   1712
  Dihedral  :  5.864  58.370   1317
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.45 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.25), residues: 1199
  helix:  0.60 (0.20), residues: 725
  sheet: -0.92 (0.76), residues: 54
  loop : -2.69 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG T 140 
 TYR   0.017   0.002   TYR K 179 
 PHE   0.019   0.002   PHE K 267 
 TRP   0.011   0.002   TRP T 339 
 HIS   0.006   0.001   HIS K 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (10171)
  covalent geometry    : angle       0.64367 (13730)
  hydrogen bonds       : bond        0.04002 (  492)
  hydrogen bonds       : angle       4.31816 ( 1452)
  metal coordination   : bond        0.00770 (    7)
  metal coordination   : angle       3.57198 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: K  280 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7834 (ttpp)
REVERT: T   39 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7974 (tp40)
REVERT: T   78 MET cc_start: 0.7960 (tmm) cc_final: 0.7732 (tpp)
REVERT: T  141 MET cc_start: 0.7596 (tmm) cc_final: 0.7137 (ptp)
REVERT: T  449 ARG cc_start: 0.8795 (tpt90) cc_final: 0.8471 (tpt90)
REVERT: T  822 MET cc_start: 0.8538 (ttp) cc_final: 0.8309 (ttt)
REVERT: T  955 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8217 (mm)
  outliers start: 32
  outliers final: 22
  residues processed: 152
  average time/residue: 0.0955
  time to fit residues: 21.3886
Evaluate side-chains
  149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  284 THR
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  380 VAL
Chi-restraints excluded: chain T residue   17 ILE
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  144 ILE
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  938 VAL
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 119 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0170
   chunk 85 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 113 optimal weight:    0.5980
   chunk 44 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.9422

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

Flipped N/Q/H residues before XYZ refinement:
K 329 HIS
K 374 ASN
T  39 GLN
T 154 ASN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 940 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.164729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.134339 restraints weight = 13530.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.138680 restraints weight = 7914.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140573 restraints weight = 5376.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.140842 restraints weight = 4226.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.141321 restraints weight = 4213.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10178  Z= 0.128
  Angle     :  0.568   9.904  13733  Z= 0.299
  Chirality :  0.042   0.292   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  5.397  61.221   1314
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.25 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.25), residues: 1199
  helix:  0.88 (0.20), residues: 718
  sheet: -0.78 (0.76), residues: 54
  loop : -2.51 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG T 140 
 TYR   0.016   0.001   TYR T 461 
 PHE   0.025   0.001   PHE K 267 
 TRP   0.011   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10171)
  covalent geometry    : angle       0.56647 (13730)
  hydrogen bonds       : bond        0.03352 (  492)
  hydrogen bonds       : angle       4.06857 ( 1452)
  metal coordination   : bond        0.01133 (    7)
  metal coordination   : angle       3.02289 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 137
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8401 (p90) cc_final: 0.8189 (p90)
REVERT: K  280 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7838 (ttpp)
REVERT: T   39 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8071 (tp40)
REVERT: T  138 PHE cc_start: 0.7953 (t80) cc_final: 0.7734 (t80)
REVERT: T  141 MET cc_start: 0.7411 (tmm) cc_final: 0.6972 (ptp)
REVERT: T  319 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7596 (mm)
REVERT: T  449 ARG cc_start: 0.8708 (tpt90) cc_final: 0.8391 (tpt90)
REVERT: T  822 MET cc_start: 0.8571 (ttp) cc_final: 0.8328 (ttt)
  outliers start: 32
  outliers final: 23
  residues processed: 152
  average time/residue: 0.0976
  time to fit residues: 21.6063
Evaluate side-chains
  154 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  380 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain K residue  437 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  144 ILE
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  171 MET
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  319 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 101 optimal weight:    0.1980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
T   2 GLN
T  28 ASN
T  39 GLN
T 154 ASN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 940 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.164364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134908 restraints weight = 13505.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.138845 restraints weight = 8286.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141302 restraints weight = 5409.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141396 restraints weight = 4259.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.141652 restraints weight = 4005.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10178  Z= 0.144
  Angle     :  0.575   8.413  13733  Z= 0.301
  Chirality :  0.042   0.271   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  5.278  60.175   1314
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.61 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.25), residues: 1199
  helix:  0.97 (0.20), residues: 718
  sheet: -1.33 (0.71), residues: 61
  loop : -2.47 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG T 140 
 TYR   0.016   0.001   TYR T 461 
 PHE   0.029   0.001   PHE T 826 
 TRP   0.011   0.001   TRP T 339 
 HIS   0.004   0.001   HIS K 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10171)
  covalent geometry    : angle       0.57328 (13730)
  hydrogen bonds       : bond        0.03292 (  492)
  hydrogen bonds       : angle       4.02293 ( 1452)
  metal coordination   : bond        0.00827 (    7)
  metal coordination   : angle       2.66097 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8451 (p90) cc_final: 0.8221 (p90)
REVERT: K  280 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7832 (ttpp)
REVERT: K  315 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7133 (p0)
REVERT: T  138 PHE cc_start: 0.7917 (t80) cc_final: 0.7662 (t80)
REVERT: T  141 MET cc_start: 0.7333 (tmm) cc_final: 0.7073 (ptt)
REVERT: T  319 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7676 (mm)
  outliers start: 34
  outliers final: 27
  residues processed: 158
  average time/residue: 0.0800
  time to fit residues: 18.8195
Evaluate side-chains
  159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  380 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  171 MET
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  319 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
K 374 ASN
T  28 ASN
T  39 GLN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 940 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.163728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.134609 restraints weight = 13487.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.138333 restraints weight = 8123.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.140260 restraints weight = 5496.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.140668 restraints weight = 4466.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140870 restraints weight = 4074.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10178  Z= 0.150
  Angle     :  0.581  10.137  13733  Z= 0.303
  Chirality :  0.042   0.256   1570
  Planarity :  0.003   0.046   1712
  Dihedral  :  5.249  61.433   1314
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.97 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.25), residues: 1199
  helix:  0.96 (0.20), residues: 722
  sheet: -1.31 (0.71), residues: 61
  loop : -2.49 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG T 140 
 TYR   0.018   0.001   TYR T 461 
 PHE   0.023   0.001   PHE T 826 
 TRP   0.010   0.001   TRP T 339 
 HIS   0.004   0.001   HIS K 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10171)
  covalent geometry    : angle       0.57942 (13730)
  hydrogen bonds       : bond        0.03306 (  492)
  hydrogen bonds       : angle       4.03448 ( 1452)
  metal coordination   : bond        0.00838 (    7)
  metal coordination   : angle       2.58670 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8458 (p90) cc_final: 0.8215 (p90)
REVERT: K  280 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7866 (ttpp)
REVERT: K  315 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7145 (p0)
REVERT: T  319 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7693 (mm)
REVERT: T  441 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8293 (mt)
REVERT: T  644 ASP cc_start: 0.7887 (t70) cc_final: 0.7338 (t0)
  outliers start: 44
  outliers final: 35
  residues processed: 161
  average time/residue: 0.0714
  time to fit residues: 17.2582
Evaluate side-chains
  168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain K residue  437 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue   74 VAL
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  112 HIS
Chi-restraints excluded: chain T residue  144 ILE
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  171 MET
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  319 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  441 LEU
Chi-restraints excluded: chain T residue  460 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
Chi-restraints excluded: chain T residue  678 ASP
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 112 optimal weight:    0.2980
   chunk 101 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 59 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
T  27 ASN
T  28 ASN
T  39 GLN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** 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 = 0.4045 r_free = 0.4045 target = 0.167143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.137974 restraints weight = 13408.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.142449 restraints weight = 8568.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.143636 restraints weight = 5309.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.144425 restraints weight = 4251.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.144644 restraints weight = 4084.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10178  Z= 0.112
  Angle     :  0.551   9.309  13733  Z= 0.288
  Chirality :  0.041   0.377   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  4.993  59.626   1313
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.96 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.25), residues: 1199
  helix:  1.07 (0.20), residues: 725
  sheet: -1.08 (0.72), residues: 61
  loop : -2.49 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG T 140 
 TYR   0.021   0.001   TYR T 461 
 PHE   0.031   0.001   PHE T 826 
 TRP   0.011   0.001   TRP T 339 
 HIS   0.006   0.001   HIS K 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10171)
  covalent geometry    : angle       0.54956 (13730)
  hydrogen bonds       : bond        0.02900 (  492)
  hydrogen bonds       : angle       3.87979 ( 1452)
  metal coordination   : bond        0.01836 (    7)
  metal coordination   : angle       2.76413 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  280 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7864 (ttpp)
REVERT: K  315 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7062 (p0)
REVERT: T  141 MET cc_start: 0.7403 (tmm) cc_final: 0.6793 (ptp)
REVERT: T  813 GLU cc_start: 0.7353 (mp0) cc_final: 0.6900 (mp0)
  outliers start: 38
  outliers final: 30
  residues processed: 170
  average time/residue: 0.0913
  time to fit residues: 22.7588
Evaluate side-chains
  166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain K residue  437 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue   74 VAL
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  460 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 120 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 94 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
T  27 ASN
T  28 ASN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.167854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.137401 restraints weight = 13354.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.141694 restraints weight = 7369.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.144493 restraints weight = 5056.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146063 restraints weight = 3927.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.147375 restraints weight = 3337.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10178  Z= 0.116
  Angle     :  0.577   9.153  13733  Z= 0.297
  Chirality :  0.042   0.373   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  4.980  59.989   1313
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.23 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.25), residues: 1199
  helix:  1.07 (0.20), residues: 729
  sheet: -0.97 (0.73), residues: 61
  loop : -2.51 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG T 140 
 TYR   0.021   0.001   TYR T 461 
 PHE   0.026   0.001   PHE T 826 
 TRP   0.010   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10171)
  covalent geometry    : angle       0.57603 (13730)
  hydrogen bonds       : bond        0.02931 (  492)
  hydrogen bonds       : angle       3.86466 ( 1452)
  metal coordination   : bond        0.01493 (    7)
  metal coordination   : angle       2.44323 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 140
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  280 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7849 (ttpp)
REVERT: K  315 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7150 (p0)
REVERT: T  141 MET cc_start: 0.7348 (tmm) cc_final: 0.7027 (ptp)
REVERT: T  813 GLU cc_start: 0.7458 (mp0) cc_final: 0.7011 (mp0)
  outliers start: 40
  outliers final: 32
  residues processed: 162
  average time/residue: 0.0893
  time to fit residues: 21.4441
Evaluate side-chains
  165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue   74 VAL
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  460 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
Chi-restraints excluded: chain T residue  691 ILE
Chi-restraints excluded: chain T residue  938 VAL
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0020
   chunk 66 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6750

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

Flipped N/Q/H residues before XYZ refinement:
T  27 ASN
T  28 ASN
T  39 GLN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.168394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139327 restraints weight = 13261.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143008 restraints weight = 7562.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.144247 restraints weight = 5128.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144651 restraints weight = 4483.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.144950 restraints weight = 4330.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10178  Z= 0.118
  Angle     :  0.578   9.080  13733  Z= 0.298
  Chirality :  0.042   0.388   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  4.866  57.554   1313
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.86 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.25), residues: 1199
  helix:  1.19 (0.20), residues: 729
  sheet: -0.88 (0.73), residues: 61
  loop : -2.51 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG T 140 
 TYR   0.022   0.001   TYR T 461 
 PHE   0.020   0.001   PHE T 541 
 TRP   0.011   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10171)
  covalent geometry    : angle       0.57699 (13730)
  hydrogen bonds       : bond        0.02889 (  492)
  hydrogen bonds       : angle       3.84626 ( 1452)
  metal coordination   : bond        0.01441 (    7)
  metal coordination   : angle       2.39386 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  280 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7825 (ttpp)
REVERT: K  315 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7111 (p0)
REVERT: T  141 MET cc_start: 0.7481 (tmm) cc_final: 0.6925 (ptt)
REVERT: T  813 GLU cc_start: 0.7522 (mp0) cc_final: 0.7041 (mp0)
  outliers start: 38
  outliers final: 34
  residues processed: 160
  average time/residue: 0.0900
  time to fit residues: 21.5656
Evaluate side-chains
  166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue   74 VAL
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  310 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  460 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
Chi-restraints excluded: chain T residue  678 ASP
Chi-restraints excluded: chain T residue  691 ILE
Chi-restraints excluded: chain T residue  938 VAL
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
K 374 ASN
T  27 ASN
T  28 ASN
T  39 GLN
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 940 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.166485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136972 restraints weight = 13290.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.141816 restraints weight = 8853.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.143238 restraints weight = 5338.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.143879 restraints weight = 4209.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144031 restraints weight = 4068.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  10178  Z= 0.145
  Angle     :  0.614  11.417  13733  Z= 0.313
  Chirality :  0.043   0.370   1570
  Planarity :  0.003   0.048   1712
  Dihedral  :  4.960  58.838   1313
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.22 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.25), residues: 1199
  helix:  1.18 (0.20), residues: 730
  sheet: -0.88 (0.74), residues: 61
  loop : -2.51 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG T 140 
 TYR   0.025   0.001   TYR T 461 
 PHE   0.020   0.001   PHE T 541 
 TRP   0.010   0.001   TRP T 339 
 HIS   0.006   0.001   HIS K 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10171)
  covalent geometry    : angle       0.61356 (13730)
  hydrogen bonds       : bond        0.03073 (  492)
  hydrogen bonds       : angle       3.88918 ( 1452)
  metal coordination   : bond        0.01038 (    7)
  metal coordination   : angle       1.76707 (    3)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  163 MET cc_start: 0.8421 (ptt) cc_final: 0.8176 (ptt)
REVERT: K  280 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7842 (ttpp)
REVERT: K  315 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7113 (p0)
REVERT: T  141 MET cc_start: 0.7480 (tmm) cc_final: 0.6945 (ptt)
REVERT: T  813 GLU cc_start: 0.7455 (mp0) cc_final: 0.7003 (mp0)
  outliers start: 38
  outliers final: 33
  residues processed: 158
  average time/residue: 0.0878
  time to fit residues: 20.9371
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain K residue   15 VAL
Chi-restraints excluded: chain K residue   32 ASP
Chi-restraints excluded: chain K residue   39 TYR
Chi-restraints excluded: chain K residue   93 THR
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  158 VAL
Chi-restraints excluded: chain K residue  203 GLU
Chi-restraints excluded: chain K residue  303 LYS
Chi-restraints excluded: chain K residue  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
Chi-restraints excluded: chain K residue  382 MET
Chi-restraints excluded: chain T residue   39 GLN
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   52 VAL
Chi-restraints excluded: chain T residue   60 ILE
Chi-restraints excluded: chain T residue   74 VAL
Chi-restraints excluded: chain T residue  107 LEU
Chi-restraints excluded: chain T residue  158 LEU
Chi-restraints excluded: chain T residue  180 HIS
Chi-restraints excluded: chain T residue  239 VAL
Chi-restraints excluded: chain T residue  276 ILE
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  460 LEU
Chi-restraints excluded: chain T residue  507 VAL
Chi-restraints excluded: chain T residue  520 GLU
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
Chi-restraints excluded: chain T residue  678 ASP
Chi-restraints excluded: chain T residue  691 ILE
Chi-restraints excluded: chain T residue  938 VAL
Chi-restraints excluded: chain T residue  955 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 121 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0770
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.0542

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

Flipped N/Q/H residues before XYZ refinement:
** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.166480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137040 restraints weight = 13473.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.141609 restraints weight = 8826.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.142921 restraints weight = 5209.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.144019 restraints weight = 4282.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144173 restraints weight = 4051.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10178  Z= 0.141
  Angle     :  0.612  11.079  13733  Z= 0.314
  Chirality :  0.043   0.365   1570
  Planarity :  0.003   0.049   1712
  Dihedral  :  4.944  57.722   1313
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.49 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.25), residues: 1199
  helix:  1.21 (0.20), residues: 726
  sheet: -0.89 (0.74), residues: 61
  loop : -2.46 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG T 140 
 TYR   0.024   0.001   TYR T 461 
 PHE   0.019   0.001   PHE T 541 
 TRP   0.010   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10171)
  covalent geometry    : angle       0.61149 (13730)
  hydrogen bonds       : bond        0.03078 (  492)
  hydrogen bonds       : angle       3.90004 ( 1452)
  metal coordination   : bond        0.01070 (    7)
  metal coordination   : angle       1.98741 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.19 seconds
wall clock time: 27 minutes 44.43 seconds (1664.43 seconds total)