Starting phenix.real_space_refine
on Fri Feb 14 08:16:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uic_42292/02_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_42292/02_2025/8uic_42292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.109
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.74, per 1000 atoms: 0.58
  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: 2.76
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  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: 1.02
  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: 3.13

  Time building geometry restraints manager: 3.06 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.310
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.420
-------------------------------------------------------------------------------
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  10171  Z= 0.457
  Angle     :  0.971   9.993  13730  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (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
 TRP   0.033   0.002   TRP K 256 
 HIS   0.008   0.001   HIS K  73 
 PHE   0.033   0.003   PHE K 267 
 TYR   0.034   0.002   TYR K 179 
 ARG   0.016   0.001   ARG T 140 

*********************** 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  : 1.167 
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: 0.2253
  time to fit residues: 63.4531
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  : 1.201 
-------------------------------------------------------------------------------
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 103 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0030
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.167975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138049 restraints weight = 13246.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.142164 restraints weight = 7437.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.143822 restraints weight = 5088.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10171  Z= 0.182
  Angle     :  0.597   8.501  13730  Z= 0.315
  Chirality :  0.042   0.263   1570
  Planarity :  0.004   0.054   1712
  Dihedral  :  6.568  58.022   1330
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.12 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.25), residues: 1199
  helix:  0.54 (0.20), residues: 712
  sheet: -0.54 (0.76), residues: 54
  loop : -2.48 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K 256 
 HIS   0.006   0.001   HIS K 414 
 PHE   0.030   0.001   PHE K 267 
 TYR   0.013   0.001   TYR T 461 
 ARG   0.005   0.000   ARG T 140 

*********************** 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
  171 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
REVERT: K   83 ILE cc_start: 0.9008 (mm) cc_final: 0.8769 (mm)
REVERT: K   92 MET cc_start: 0.8096 (ptm) cc_final: 0.7834 (ptm)
REVERT: K  280 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7817 (ttpp)
REVERT: T  449 ARG cc_start: 0.8703 (tpt90) cc_final: 0.8366 (tpt90)
REVERT: T  746 TYR cc_start: 0.8553 (m-80) cc_final: 0.8337 (m-10)
REVERT: T  822 MET cc_start: 0.8547 (ttp) cc_final: 0.8206 (ttt)
  outliers start: 24
  outliers final: 18
  residues processed: 160
  average time/residue: 0.2032
  time to fit residues: 47.8394
Evaluate side-chains
  149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
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  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  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  955 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0670
   chunk 85 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   chunk 101 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4061 r_free = 0.4061 target = 0.168900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138113 restraints weight = 13436.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.142584 restraints weight = 7345.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.145419 restraints weight = 4995.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10171  Z= 0.165
  Angle     :  0.549   7.022  13730  Z= 0.291
  Chirality :  0.040   0.180   1570
  Planarity :  0.003   0.047   1712
  Dihedral  :  5.528  55.673   1317
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.00 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.25), residues: 1199
  helix:  0.85 (0.20), residues: 717
  sheet: -0.47 (0.77), residues: 52
  loop : -2.49 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP K 256 
 HIS   0.004   0.001   HIS K 414 
 PHE   0.020   0.001   PHE T 541 
 TYR   0.016   0.001   TYR T 271 
 ARG   0.005   0.000   ARG T 140 

*********************** 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
  177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
REVERT: K   83 ILE cc_start: 0.9033 (mm) cc_final: 0.8794 (mm)
REVERT: K   92 MET cc_start: 0.8057 (ptm) cc_final: 0.7803 (ptm)
REVERT: K  280 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7809 (ttpp)
REVERT: T   39 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7860 (tp40)
REVERT: T  141 MET cc_start: 0.7408 (tmm) cc_final: 0.6890 (ptp)
REVERT: T  319 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7498 (mm)
REVERT: T  957 ASP cc_start: 0.8193 (t0) cc_final: 0.7866 (t0)
  outliers start: 29
  outliers final: 23
  residues processed: 161
  average time/residue: 0.2122
  time to fit residues: 49.8220
Evaluate side-chains
  159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
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  303 LYS
Chi-restraints excluded: chain K residue  329 HIS
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   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  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  938 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 154 ASN
** 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 = 0.4023 r_free = 0.4023 target = 0.165348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.135032 restraints weight = 13294.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.139396 restraints weight = 7879.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.141205 restraints weight = 5258.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10171  Z= 0.255
  Angle     :  0.584   8.176  13730  Z= 0.306
  Chirality :  0.043   0.298   1570
  Planarity :  0.004   0.047   1712
  Dihedral  :  5.467  57.534   1317
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.17 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1199
  helix:  0.97 (0.21), residues: 717
  sheet: -1.24 (0.70), residues: 61
  loop : -2.46 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP T 339 
 HIS   0.006   0.001   HIS K 329 
 PHE   0.019   0.001   PHE T 541 
 TYR   0.016   0.001   TYR T 271 
 ARG   0.006   0.000   ARG T 140 

*********************** 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
  165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8445 (p90) cc_final: 0.7924 (p90)
REVERT: K  280 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7833 (ttpp)
REVERT: T   39 GLN cc_start: 0.8316 (tp40) cc_final: 0.8051 (tp40)
REVERT: T  319 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7667 (mm)
  outliers start: 29
  outliers final: 22
  residues processed: 152
  average time/residue: 0.2083
  time to fit residues: 46.3640
Evaluate side-chains
  150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  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  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  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  725 VAL
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    2.1386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.161519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132069 restraints weight = 13399.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.135666 restraints weight = 8253.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137319 restraints weight = 5642.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10171  Z= 0.350
  Angle     :  0.638   8.943  13730  Z= 0.333
  Chirality :  0.044   0.151   1570
  Planarity :  0.004   0.049   1712
  Dihedral  :  5.621  58.739   1317
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.97 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.25), residues: 1199
  helix:  0.78 (0.20), residues: 729
  sheet: -1.44 (0.70), residues: 61
  loop : -2.62 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K 414 
 PHE   0.029   0.002   PHE T 826 
 TYR   0.018   0.002   TYR T 461 
 ARG   0.007   0.000   ARG T 140 

*********************** 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
  167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8518 (p90) cc_final: 0.8184 (p90)
REVERT: K  257 GLU cc_start: 0.7606 (tp30) cc_final: 0.7401 (tp30)
REVERT: K  280 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7843 (ttpp)
REVERT: K  315 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7313 (p0)
REVERT: T   39 GLN cc_start: 0.8327 (tp40) cc_final: 0.7910 (tp40)
REVERT: T  141 MET cc_start: 0.7514 (tmm) cc_final: 0.7126 (ptp)
REVERT: T  449 ARG cc_start: 0.8724 (tpt90) cc_final: 0.8438 (tpt90)
  outliers start: 34
  outliers final: 27
  residues processed: 154
  average time/residue: 0.2264
  time to fit residues: 50.6870
Evaluate side-chains
  155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
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   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  380 VAL
Chi-restraints excluded: chain T residue   17 ILE
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  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  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 116 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 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 = 0.3995 r_free = 0.3995 target = 0.162617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.133147 restraints weight = 13494.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.138070 restraints weight = 8384.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.139296 restraints weight = 5426.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10171  Z= 0.277
  Angle     :  0.610   7.914  13730  Z= 0.318
  Chirality :  0.043   0.313   1570
  Planarity :  0.004   0.050   1712
  Dihedral  :  5.379  59.066   1314
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.06 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1199
  helix:  0.83 (0.20), residues: 729
  sheet: -1.40 (0.70), residues: 61
  loop : -2.56 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP T 339 
 HIS   0.005   0.001   HIS K 414 
 PHE   0.023   0.002   PHE T 826 
 TYR   0.019   0.001   TYR T 461 
 ARG   0.008   0.000   ARG T 140 

*********************** 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
  167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8498 (p90) cc_final: 0.8189 (p90)
REVERT: K  257 GLU cc_start: 0.7602 (tp30) cc_final: 0.7389 (tp30)
REVERT: K  280 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7867 (ttpp)
REVERT: K  315 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7296 (p0)
REVERT: T  371 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8234 (tp)
REVERT: T  441 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8320 (mt)
REVERT: T  449 ARG cc_start: 0.8677 (tpt90) cc_final: 0.8407 (tpt90)
  outliers start: 40
  outliers final: 33
  residues processed: 155
  average time/residue: 0.2064
  time to fit residues: 47.1199
Evaluate side-chains
  161 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
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  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 K residue  437 MET
Chi-restraints excluded: chain T residue   17 ILE
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  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  371 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  441 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  938 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.166250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136593 restraints weight = 13569.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140271 restraints weight = 8143.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.141562 restraints weight = 5591.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10171  Z= 0.185
  Angle     :  0.566  10.236  13730  Z= 0.296
  Chirality :  0.041   0.262   1570
  Planarity :  0.003   0.048   1712
  Dihedral  :  5.118  58.605   1314
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.51 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.25), residues: 1199
  helix:  1.04 (0.20), residues: 725
  sheet: -1.21 (0.71), residues: 61
  loop : -2.49 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 339 
 HIS   0.004   0.001   HIS K  73 
 PHE   0.031   0.001   PHE T 826 
 TYR   0.021   0.001   TYR T 461 
 ARG   0.008   0.000   ARG T 140 

*********************** 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
  182 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8492 (p90) cc_final: 0.8156 (p90)
REVERT: K  257 GLU cc_start: 0.7550 (tp30) cc_final: 0.7345 (tp30)
REVERT: K  280 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7852 (ttpp)
REVERT: K  315 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7148 (p0)
REVERT: T  141 MET cc_start: 0.7471 (tmm) cc_final: 0.6876 (ptp)
REVERT: T  319 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (mm)
REVERT: T  371 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8177 (tp)
REVERT: T  644 ASP cc_start: 0.7777 (t70) cc_final: 0.7174 (t0)
REVERT: T  813 GLU cc_start: 0.7455 (mp0) cc_final: 0.7000 (mp0)
  outliers start: 41
  outliers final: 30
  residues processed: 166
  average time/residue: 0.1907
  time to fit residues: 46.9395
Evaluate side-chains
  167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
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  315 ASN
Chi-restraints excluded: chain K residue  363 ILE
Chi-restraints excluded: chain K residue  370 VAL
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  319 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  371 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  546 THR
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  709 ILE
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 107 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.167681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138360 restraints weight = 13396.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143275 restraints weight = 8635.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.144258 restraints weight = 5272.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10171  Z= 0.174
  Angle     :  0.583  17.129  13730  Z= 0.299
  Chirality :  0.041   0.193   1570
  Planarity :  0.003   0.048   1712
  Dihedral  :  5.016  57.511   1313
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1199
  helix:  1.10 (0.20), residues: 730
  sheet: -1.04 (0.72), residues: 61
  loop : -2.49 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 339 
 HIS   0.004   0.001   HIS K  73 
 PHE   0.026   0.001   PHE T 826 
 TYR   0.021   0.001   TYR T 461 
 ARG   0.009   0.000   ARG T 140 

*********************** 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
  176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 137
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8491 (p90) cc_final: 0.8124 (p90)
REVERT: K  280 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7839 (ttpp)
REVERT: K  315 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7072 (p0)
REVERT: T  141 MET cc_start: 0.7426 (tmm) cc_final: 0.6783 (ptp)
REVERT: T  319 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (mm)
REVERT: T  813 GLU cc_start: 0.7421 (mp0) cc_final: 0.6972 (mp0)
  outliers start: 39
  outliers final: 31
  residues processed: 158
  average time/residue: 0.2104
  time to fit residues: 49.5416
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  : 1.151 
-------------------------------------------------------------------------------
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  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  319 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  546 THR
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 119 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.166162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136977 restraints weight = 13394.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.140109 restraints weight = 8259.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.141922 restraints weight = 5888.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10171  Z= 0.226
  Angle     :  0.610  16.471  13730  Z= 0.310
  Chirality :  0.043   0.386   1570
  Planarity :  0.003   0.049   1712
  Dihedral  :  5.021  57.043   1313
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.32 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.25), residues: 1199
  helix:  1.11 (0.20), residues: 729
  sheet: -1.07 (0.72), residues: 61
  loop : -2.51 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 339 
 HIS   0.007   0.001   HIS K 157 
 PHE   0.024   0.001   PHE T 826 
 TYR   0.023   0.001   TYR T 461 
 ARG   0.010   0.000   ARG T 140 

*********************** 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
  170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8519 (p90) cc_final: 0.8184 (p90)
REVERT: K  280 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7866 (ttpp)
REVERT: K  315 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7108 (p0)
REVERT: T  141 MET cc_start: 0.7449 (tmm) cc_final: 0.6826 (ptp)
REVERT: T  319 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7704 (mm)
REVERT: T  371 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8175 (tp)
REVERT: T  813 GLU cc_start: 0.7489 (mp0) cc_final: 0.7003 (mp0)
  outliers start: 38
  outliers final: 33
  residues processed: 155
  average time/residue: 0.2017
  time to fit residues: 45.6847
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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  319 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  371 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  546 THR
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
Chi-restraints excluded: chain T residue  938 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 82 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.164563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.135365 restraints weight = 13518.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139153 restraints weight = 8238.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.140563 restraints weight = 5820.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10171  Z= 0.272
  Angle     :  0.635  16.124  13730  Z= 0.323
  Chirality :  0.044   0.387   1570
  Planarity :  0.003   0.050   1712
  Dihedral  :  5.114  57.184   1313
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 1199
  helix:  1.08 (0.20), residues: 729
  sheet: -1.11 (0.73), residues: 61
  loop : -2.56 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP T 339 
 HIS   0.007   0.001   HIS K 157 
 PHE   0.036   0.001   PHE T 826 
 TYR   0.024   0.001   TYR T 461 
 ARG   0.011   0.000   ARG T 140 

********************** 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
  168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
REVERT: K  179 TYR cc_start: 0.8564 (p90) cc_final: 0.8172 (p90)
REVERT: K  280 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7826 (ttpp)
REVERT: K  315 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7161 (p0)
REVERT: T  141 MET cc_start: 0.7449 (tmm) cc_final: 0.6868 (ptp)
REVERT: T  319 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7755 (mm)
REVERT: T  371 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8224 (tp)
REVERT: T  813 GLU cc_start: 0.7488 (mp0) cc_final: 0.7018 (mp0)
  outliers start: 41
  outliers final: 34
  residues processed: 153
  average time/residue: 0.1957
  time to fit residues: 44.1015
Evaluate side-chains
  158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
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  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  319 LEU
Chi-restraints excluded: chain T residue  342 LEU
Chi-restraints excluded: chain T residue  371 LEU
Chi-restraints excluded: chain T residue  409 LEU
Chi-restraints excluded: chain T residue  443 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  546 THR
Chi-restraints excluded: chain T residue  562 LEU
Chi-restraints excluded: chain T residue  661 VAL
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 52 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.166550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137771 restraints weight = 13409.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.140500 restraints weight = 8380.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.141991 restraints weight = 5865.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10171  Z= 0.208
  Angle     :  0.615  16.074  13730  Z= 0.313
  Chirality :  0.043   0.389   1570
  Planarity :  0.003   0.049   1712
  Dihedral  :  5.034  56.521   1313
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.59 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.25), residues: 1199
  helix:  1.12 (0.20), residues: 730
  sheet: -0.94 (0.75), residues: 61
  loop : -2.51 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 339 
 HIS   0.006   0.001   HIS K 157 
 PHE   0.036   0.001   PHE T 826 
 TYR   0.025   0.001   TYR T 461 
 ARG   0.011   0.000   ARG T 140 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2692.59 seconds
wall clock time: 49 minutes 21.58 seconds (2961.58 seconds total)