Starting phenix.real_space_refine
on Tue Mar  3 18:00:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk3_21224/03_2026/6vk3_21224.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4967      2.51       5
     N    1303      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7784
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1906
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3060
          Classifications: {'peptide': 381}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 369}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2818
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 10, 'TRANS': 339}
          Chain breaks: 2
  Time building chain proxies: 1.44, per 1000 atoms: 0.18
  Number of scatterers: 7784
  At special positions: 0
  Unit cell: (103.88, 101.76, 103.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1476      8.00
     N    1303      7.00
     C    4967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS B 258 " distance=2.81
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 130 " distance=2.50
    Simple disulfide: pdb=" SG  CYS B 193 " - pdb=" SG  CYS B 227 " distance=2.87
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 239 " distance=2.21

  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: 0.62
  Conformation dependent library (CDL) restraints added in 276.9 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      55.3% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 42 through 47
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 124 through 139
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.612A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 3.604A  pdb=" N   TYR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 314 through 331
      removed outlier: 4.074A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 356 through 358
      No H-bonds generated for 'chain 'A' and resid 356 through 358'
    Processing helix  chain 'A' and resid 362 through 383
    Processing helix  chain 'A' and resid 390 through 407
    Processing helix  chain 'A' and resid 412 through 423
    Processing helix  chain 'A' and resid 429 through 442
      removed outlier: 4.813A  pdb=" N   LYS A 442 " --> pdb=" O   MET A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 3.907A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 465'
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 494
      removed outlier: 3.615A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 4.190A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 4.119A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 550
      removed outlier: 3.539A  pdb=" N   LEU A 540 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN A 549 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.874A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 609
      removed outlier: 4.113A  pdb=" N   GLY A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 624
      removed outlier: 3.750A  pdb=" N   ALA A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 640
      removed outlier: 3.516A  pdb=" N   HIS A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.714A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 684
    Processing helix  chain 'B' and resid 41 through 49
      removed outlier: 3.637A  pdb=" N   ILE B  49 " --> pdb=" O   TRP B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.785A  pdb=" N   MET B  56 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 114
    Processing helix  chain 'B' and resid 236 through 245
      removed outlier: 3.524A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 237 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   GLU B 242 " --> pdb=" O   CYS B 239 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU B 243 " --> pdb=" O   ASN B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.688A  pdb=" N   TYR B 318 " --> pdb=" O   THR B 314 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62
      removed outlier: 7.068A  pdb=" N   VAL A  61 " --> pdb=" O   UNK A 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 40
      removed outlier: 6.193A  pdb=" N   LEU B  36 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   CYS B 258 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   SER B  38 " --> pdb=" O   CYS B 258 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 122
      removed outlier: 3.962A  pdb=" N   VAL B 136 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 176
      removed outlier: 8.895A  pdb=" N   TYR B 181 " --> pdb=" O   CYS B 208 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   CYS B 208 " --> pdb=" O   TYR B 181 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR B 229 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TRP B 220 " --> pdb=" O   GLN B 232 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR B 234 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   ILE B 218 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 277 through 278
      removed outlier: 3.528A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR B 363 " --> pdb=" O   VAL B 354 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASN B 368 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   GLU B 376 " --> pdb=" O   ASN B 368 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 277 through 278
      removed outlier: 3.528A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2453
        1.34 -     1.46: 1438
        1.46 -     1.58: 4006
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 7960
  Sorted by residual:
  bond pdb=" C   ARG B 116 "
       pdb=" N   CYS B 117 "
    ideal  model  delta    sigma   weight residual
    1.330  1.235  0.095 1.38e-02 5.25e+03 4.71e+01
  bond pdb=" C   CYS B 117 "
       pdb=" N   ILE B 118 "
    ideal  model  delta    sigma   weight residual
    1.333  1.248  0.085 1.34e-02 5.57e+03 4.04e+01
  bond pdb=" CE1 HIS B 139 "
       pdb=" NE2 HIS B 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.25e+00
  bond pdb=" N   VAL B 179 "
       pdb=" CA  VAL B 179 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.19e-02 7.06e+03 8.57e+00
  bond pdb=" N   TYR B 181 "
       pdb=" CA  TYR B 181 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.31e-02 5.83e+03 8.52e+00
  ... (remaining 7955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 10108
        1.86 -     3.72: 557
        3.72 -     5.58: 84
        5.58 -     7.44: 21
        7.44 -     9.30: 1
  Bond angle restraints: 10771
  Sorted by residual:
  angle pdb=" N   LEU B  68 "
        pdb=" CA  LEU B  68 "
        pdb=" C   LEU B  68 "
      ideal   model   delta    sigma   weight residual
     112.41  105.55    6.86 1.30e+00 5.92e-01 2.79e+01
  angle pdb=" C   LEU B 241 "
        pdb=" N   GLU B 242 "
        pdb=" CA  GLU B 242 "
      ideal   model   delta    sigma   weight residual
     120.54  126.97   -6.43 1.35e+00 5.49e-01 2.27e+01
  angle pdb=" CA  ASN B 166 "
        pdb=" CB  ASN B 166 "
        pdb=" CG  ASN B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  117.34   -4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" C   CYS B 130 "
        pdb=" N   PRO B 131 "
        pdb=" CA  PRO B 131 "
      ideal   model   delta    sigma   weight residual
     119.84  125.42   -5.58 1.25e+00 6.40e-01 1.99e+01
  angle pdb=" N   GLU B 242 "
        pdb=" CA  GLU B 242 "
        pdb=" CB  GLU B 242 "
      ideal   model   delta    sigma   weight residual
     109.94  103.38    6.56 1.49e+00 4.50e-01 1.94e+01
  ... (remaining 10766 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 4189
       16.84 -    33.68: 446
       33.68 -    50.52: 98
       50.52 -    67.36: 18
       67.36 -    84.21: 14
  Dihedral angle restraints: 4765
    sinusoidal: 1921
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  ASN A 516 "
           pdb=" C   ASN A 516 "
           pdb=" N   GLU A 517 "
           pdb=" CA  GLU A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CB  CYS B 208 "
           pdb=" SG  CYS B 208 "
           pdb=" SG  CYS B 239 "
           pdb=" CB  CYS B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.09   39.09     1      1.00e+01 1.00e-02 2.15e+01
  dihedral pdb=" CA  ASN A 533 "
           pdb=" C   ASN A 533 "
           pdb=" N   ASP A 534 "
           pdb=" CA  ASP A 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.45   21.55     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 4762 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 949
       0.065 -    0.129: 165
       0.129 -    0.194: 39
       0.194 -    0.259: 5
       0.259 -    0.324: 2
  Chirality restraints: 1160
  Sorted by residual:
  chirality pdb=" CB  THR B 224 "
            pdb=" CA  THR B 224 "
            pdb=" OG1 THR B 224 "
            pdb=" CG2 THR B 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  ARG B 116 "
            pdb=" N   ARG B 116 "
            pdb=" C   ARG B 116 "
            pdb=" CB  ARG B 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CB  THR B 196 "
            pdb=" CA  THR B 196 "
            pdb=" OG1 THR B 196 "
            pdb=" CG2 THR B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1157 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 125 "    0.209 2.00e-02 2.50e+03   1.05e-01 2.77e+02
        pdb=" CG  TRP B 125 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 125 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 125 "   -0.112 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 125 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 125 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 125 "   -0.135 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 125 "    0.119 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 125 "   -0.037 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 125 "    0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 129 "    0.077 2.00e-02 2.50e+03   4.94e-02 4.88e+01
        pdb=" CG  TYR B 129 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 129 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 129 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 129 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 129 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 129 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR B 129 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 110 "   -0.048 2.00e-02 2.50e+03   3.06e-02 1.63e+01
        pdb=" CG  PHE B 110 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 110 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 110 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 110 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 110 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 78
        2.59 -     3.17: 6732
        3.17 -     3.75: 11739
        3.75 -     4.32: 15926
        4.32 -     4.90: 26692
  Nonbonded interactions: 61167
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 309 "
            pdb=" OD1 ASN B 309 "
     model   vdw
     2.013 3.040
  nonbonded pdb=" NE2 GLN B 250 "
            pdb=" ND2 ASN B 252 "
     model   vdw
     2.245 3.200
  nonbonded pdb=" OG  SER A  97 "
            pdb=" OG1 THR A 106 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NZ  LYS A 456 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" CB  PRO B  25 "
            pdb=" OH  TYR B 176 "
     model   vdw
     2.307 3.440
  ... (remaining 61162 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.015   0.834   7964  Z= 0.766
  Angle     :  0.999  29.627  10779  Z= 0.611
  Chirality :  0.056   0.324   1160
  Planarity :  0.007   0.105   1384
  Dihedral  : 14.845  84.206   2925
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.11 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.24), residues: 940
  helix: -0.92 (0.20), residues: 499
  sheet: -1.96 (0.59), residues: 74
  loop : -2.76 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 152 
 TYR   0.086   0.002   TYR B 129 
 PHE   0.048   0.004   PHE B 110 
 TRP   0.209   0.008   TRP B 125 
 HIS   0.008   0.001   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 7960)
  covalent geometry    : angle       0.93391 (10771)
  SS BOND              : bond        0.62244 (    4)
  SS BOND              : angle      13.03753 (    8)
  hydrogen bonds       : bond        0.14596 (  405)
  hydrogen bonds       : angle       6.45916 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8370 (m-30) cc_final: 0.8134 (m-30)
REVERT: A  238 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8015 (mp0)
REVERT: A  670 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6488 (mmtt)
REVERT: A  675 LYS cc_start: 0.8677 (tptm) cc_final: 0.7924 (tmmt)
REVERT: B   64 MET cc_start: 0.8875 (mmt) cc_final: 0.8590 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0974
  time to fit residues: 18.2215
Evaluate side-chains
  98 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0470
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 123 ASN
A 202 ASN
A 208 HIS
B 121 GLN
B 309 ASN
B 326 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.196713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.146627 restraints weight = 9904.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.142369 restraints weight = 9647.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.145325 restraints weight = 9803.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.145245 restraints weight = 5889.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.145801 restraints weight = 5623.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7964  Z= 0.122
  Angle     :  0.537   6.759  10779  Z= 0.288
  Chirality :  0.040   0.145   1160
  Planarity :  0.003   0.042   1384
  Dihedral  :  4.365  21.905   1060
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.60 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.27), residues: 940
  helix:  0.60 (0.23), residues: 501
  sheet: -1.73 (0.51), residues: 91
  loop : -2.09 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 200 
 TYR   0.010   0.001   TYR B 182 
 PHE   0.015   0.001   PHE A 201 
 TRP   0.008   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7960)
  covalent geometry    : angle       0.53679 (10771)
  SS BOND              : bond        0.00590 (    4)
  SS BOND              : angle       0.83859 (    8)
  hydrogen bonds       : bond        0.03936 (  405)
  hydrogen bonds       : angle       4.55160 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7764 (mmm) cc_final: 0.7448 (mmm)
REVERT: A  136 ASP cc_start: 0.8380 (m-30) cc_final: 0.8146 (m-30)
REVERT: A  183 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8039 (mm-40)
REVERT: A  347 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8436 (mm)
REVERT: A  639 GLU cc_start: 0.8764 (pp20) cc_final: 0.8246 (tt0)
REVERT: A  670 LYS cc_start: 0.6826 (mmtt) cc_final: 0.6268 (mmtt)
REVERT: B   64 MET cc_start: 0.8892 (mmt) cc_final: 0.8657 (mmp)
REVERT: B  278 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8266 (tm-30)
REVERT: B  309 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7525 (p0)
  outliers start: 21
  outliers final: 10
  residues processed: 146
  average time/residue: 0.0783
  time to fit residues: 15.9961
Evaluate side-chains
  118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.194096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142292 restraints weight = 9795.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.139291 restraints weight = 9828.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.141334 restraints weight = 9206.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.141891 restraints weight = 6290.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.141891 restraints weight = 5955.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7964  Z= 0.153
  Angle     :  0.533   8.915  10779  Z= 0.281
  Chirality :  0.040   0.183   1160
  Planarity :  0.003   0.040   1384
  Dihedral  :  4.270  22.122   1060
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.17 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.27), residues: 940
  helix:  1.01 (0.23), residues: 504
  sheet: -1.44 (0.58), residues: 79
  loop : -1.94 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 200 
 TYR   0.008   0.001   TYR A  65 
 PHE   0.012   0.001   PHE A 367 
 TRP   0.005   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7960)
  covalent geometry    : angle       0.53269 (10771)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.59715 (    8)
  hydrogen bonds       : bond        0.03913 (  405)
  hydrogen bonds       : angle       4.35954 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8035 (mm-40)
REVERT: A  347 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8450 (mm)
REVERT: A  390 ASN cc_start: 0.8777 (m-40) cc_final: 0.8363 (t0)
REVERT: A  670 LYS cc_start: 0.6833 (mmtt) cc_final: 0.6335 (mmtt)
REVERT: B   64 MET cc_start: 0.8931 (mmt) cc_final: 0.8682 (mmp)
REVERT: B  134 GLU cc_start: 0.1722 (OUTLIER) cc_final: 0.1320 (pp20)
REVERT: B  175 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5969 (mp)
REVERT: B  287 TYR cc_start: 0.9105 (m-80) cc_final: 0.8840 (m-80)
  outliers start: 27
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0652
  time to fit residues: 12.2358
Evaluate side-chains
  121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 78 optimal weight:   20.0000
   chunk 85 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.191659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.140668 restraints weight = 9977.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.136827 restraints weight = 10650.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.139357 restraints weight = 9957.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.139501 restraints weight = 6595.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.139654 restraints weight = 6532.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7964  Z= 0.202
  Angle     :  0.565   9.050  10779  Z= 0.296
  Chirality :  0.041   0.179   1160
  Planarity :  0.003   0.045   1384
  Dihedral  :  4.370  22.563   1060
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.48 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.27), residues: 940
  helix:  1.15 (0.23), residues: 504
  sheet: -1.42 (0.59), residues: 79
  loop : -1.84 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 265 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.011   0.001   PHE A 452 
 TRP   0.013   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7960)
  covalent geometry    : angle       0.56515 (10771)
  SS BOND              : bond        0.00161 (    4)
  SS BOND              : angle       0.74589 (    8)
  hydrogen bonds       : bond        0.04048 (  405)
  hydrogen bonds       : angle       4.45828 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8436 (m-30) cc_final: 0.8185 (m-30)
REVERT: A  183 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8021 (mm-40)
REVERT: A  347 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8428 (mm)
REVERT: A  380 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8033 (m-10)
REVERT: A  670 LYS cc_start: 0.6840 (mmtt) cc_final: 0.6267 (mmtt)
REVERT: B   64 MET cc_start: 0.8980 (mmt) cc_final: 0.8692 (mmp)
REVERT: B  175 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.6055 (mp)
REVERT: B  216 SER cc_start: 0.2054 (OUTLIER) cc_final: 0.1064 (t)
REVERT: B  278 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8316 (tm-30)
  outliers start: 31
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0711
  time to fit residues: 13.7570
Evaluate side-chains
  122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 34 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.194291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.143681 restraints weight = 9906.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142145 restraints weight = 10076.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.144310 restraints weight = 9180.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.144431 restraints weight = 6604.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.145231 restraints weight = 6558.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7964  Z= 0.144
  Angle     :  0.521   7.746  10779  Z= 0.273
  Chirality :  0.039   0.161   1160
  Planarity :  0.003   0.042   1384
  Dihedral  :  4.206  21.265   1060
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 18.79 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.28), residues: 940
  helix:  1.39 (0.23), residues: 504
  sheet: -1.25 (0.60), residues: 79
  loop : -1.76 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.010   0.001   PHE A 452 
 TRP   0.008   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7960)
  covalent geometry    : angle       0.52081 (10771)
  SS BOND              : bond        0.00150 (    4)
  SS BOND              : angle       0.65899 (    8)
  hydrogen bonds       : bond        0.03640 (  405)
  hydrogen bonds       : angle       4.23830 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8406 (m-30) cc_final: 0.8152 (m-30)
REVERT: A  152 MET cc_start: 0.8842 (ttm) cc_final: 0.8536 (mtp)
REVERT: A  183 GLN cc_start: 0.8230 (mt0) cc_final: 0.7897 (mm-40)
REVERT: A  347 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8342 (mm)
REVERT: A  380 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7992 (m-10)
REVERT: A  444 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7839 (tp40)
REVERT: A  611 ASN cc_start: 0.7575 (t0) cc_final: 0.7345 (m-40)
REVERT: A  639 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8325 (tt0)
REVERT: A  670 LYS cc_start: 0.6651 (mmtt) cc_final: 0.6131 (mmtt)
REVERT: B   64 MET cc_start: 0.8951 (mmt) cc_final: 0.8690 (mmt)
REVERT: B  175 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5964 (mp)
REVERT: B  216 SER cc_start: 0.2396 (OUTLIER) cc_final: 0.1438 (t)
REVERT: B  278 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: B  287 TYR cc_start: 0.9137 (m-80) cc_final: 0.8847 (m-80)
  outliers start: 35
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0678
  time to fit residues: 13.3518
Evaluate side-chains
  133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0980
   chunk 31 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.195316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.145763 restraints weight = 9937.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.143078 restraints weight = 10562.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.145954 restraints weight = 10076.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.145661 restraints weight = 6572.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.146167 restraints weight = 6220.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7964  Z= 0.126
  Angle     :  0.517  10.507  10779  Z= 0.269
  Chirality :  0.039   0.154   1160
  Planarity :  0.003   0.048   1384
  Dihedral  :  4.103  20.491   1060
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.57 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.28), residues: 940
  helix:  1.53 (0.23), residues: 505
  sheet: -1.18 (0.60), residues: 79
  loop : -1.66 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.008   0.001   PHE A 452 
 TRP   0.016   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7960)
  covalent geometry    : angle       0.51692 (10771)
  SS BOND              : bond        0.00122 (    4)
  SS BOND              : angle       0.67729 (    8)
  hydrogen bonds       : bond        0.03471 (  405)
  hydrogen bonds       : angle       4.15053 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8875 (ttm) cc_final: 0.8517 (mtp)
REVERT: A  183 GLN cc_start: 0.8133 (mt0) cc_final: 0.7786 (mm-40)
REVERT: A  347 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  348 GLU cc_start: 0.7556 (tp30) cc_final: 0.7227 (tp30)
REVERT: A  380 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.7835 (m-10)
REVERT: A  390 ASN cc_start: 0.8726 (m-40) cc_final: 0.8435 (t0)
REVERT: A  444 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7847 (tp40)
REVERT: A  611 ASN cc_start: 0.7442 (t0) cc_final: 0.7189 (m-40)
REVERT: A  639 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8179 (tt0)
REVERT: A  642 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7196 (pp)
REVERT: B   64 MET cc_start: 0.8952 (mmt) cc_final: 0.8700 (mmp)
REVERT: B  216 SER cc_start: 0.2651 (OUTLIER) cc_final: 0.1707 (t)
REVERT: B  278 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: B  287 TYR cc_start: 0.9133 (m-80) cc_final: 0.8842 (m-80)
REVERT: B  396 LYS cc_start: 0.4293 (pttt) cc_final: 0.4068 (pttt)
  outliers start: 27
  outliers final: 18
  residues processed: 136
  average time/residue: 0.0740
  time to fit residues: 14.3542
Evaluate side-chains
  131 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 92 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0570
   chunk 26 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.197894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.147426 restraints weight = 9954.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.147237 restraints weight = 10083.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.148832 restraints weight = 8876.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.148902 restraints weight = 6232.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.149469 restraints weight = 5849.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7964  Z= 0.149
  Angle     :  0.535   9.635  10779  Z= 0.278
  Chirality :  0.040   0.156   1160
  Planarity :  0.003   0.048   1384
  Dihedral  :  4.104  20.962   1060
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 20.45 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.28), residues: 940
  helix:  1.55 (0.23), residues: 504
  sheet: -1.20 (0.59), residues: 79
  loop : -1.61 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 200 
 TYR   0.010   0.001   TYR A 368 
 PHE   0.009   0.001   PHE A 452 
 TRP   0.017   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7960)
  covalent geometry    : angle       0.53433 (10771)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       0.74075 (    8)
  hydrogen bonds       : bond        0.03589 (  405)
  hydrogen bonds       : angle       4.20761 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8865 (ttm) cc_final: 0.8524 (mtp)
REVERT: A  347 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8440 (mm)
REVERT: A  348 GLU cc_start: 0.7656 (tp30) cc_final: 0.7353 (tp30)
REVERT: A  380 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7832 (m-10)
REVERT: A  444 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7894 (tp40)
REVERT: A  478 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9227 (mm)
REVERT: A  611 ASN cc_start: 0.7553 (t0) cc_final: 0.7328 (m-40)
REVERT: A  639 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8311 (tt0)
REVERT: A  642 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7328 (pp)
REVERT: B   64 MET cc_start: 0.8943 (mmt) cc_final: 0.8689 (mmp)
REVERT: B  216 SER cc_start: 0.2786 (OUTLIER) cc_final: 0.1862 (t)
REVERT: B  278 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8343 (tm-30)
REVERT: B  287 TYR cc_start: 0.9162 (m-80) cc_final: 0.8865 (m-80)
REVERT: B  396 LYS cc_start: 0.4207 (pttt) cc_final: 0.3977 (pttt)
  outliers start: 37
  outliers final: 21
  residues processed: 145
  average time/residue: 0.0806
  time to fit residues: 16.2983
Evaluate side-chains
  134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 94 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.199414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.150051 restraints weight = 9975.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.150483 restraints weight = 10174.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.151952 restraints weight = 8433.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152033 restraints weight = 5997.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.152527 restraints weight = 5940.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7964  Z= 0.132
  Angle     :  0.529   9.354  10779  Z= 0.274
  Chirality :  0.039   0.154   1160
  Planarity :  0.003   0.048   1384
  Dihedral  :  4.067  20.312   1060
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 20.33 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.28), residues: 940
  helix:  1.60 (0.23), residues: 505
  sheet: -1.15 (0.59), residues: 79
  loop : -1.58 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.009   0.001   PHE A 452 
 TRP   0.018   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7960)
  covalent geometry    : angle       0.52893 (10771)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       0.85635 (    8)
  hydrogen bonds       : bond        0.03451 (  405)
  hydrogen bonds       : angle       4.16501 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8861 (ttm) cc_final: 0.8508 (mtp)
REVERT: A  347 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  348 GLU cc_start: 0.7742 (tp30) cc_final: 0.7436 (tp30)
REVERT: A  380 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7913 (m-10)
REVERT: A  390 ASN cc_start: 0.8739 (m-40) cc_final: 0.8424 (t0)
REVERT: A  428 ASN cc_start: 0.7357 (m110) cc_final: 0.6694 (t0)
REVERT: A  444 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7883 (tp40)
REVERT: A  478 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9209 (mm)
REVERT: A  611 ASN cc_start: 0.7469 (t0) cc_final: 0.7227 (m-40)
REVERT: A  639 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8315 (tt0)
REVERT: B   64 MET cc_start: 0.8947 (mmt) cc_final: 0.8692 (mmp)
REVERT: B  203 GLU cc_start: 0.2929 (OUTLIER) cc_final: 0.2685 (tm-30)
REVERT: B  216 SER cc_start: 0.2470 (OUTLIER) cc_final: 0.1544 (t)
REVERT: B  278 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8310 (tm-30)
REVERT: B  287 TYR cc_start: 0.9170 (m-80) cc_final: 0.8885 (m-80)
REVERT: B  353 GLU cc_start: 0.8203 (mp0) cc_final: 0.7859 (pt0)
REVERT: B  396 LYS cc_start: 0.4253 (pttt) cc_final: 0.4020 (pttt)
  outliers start: 33
  outliers final: 23
  residues processed: 141
  average time/residue: 0.0763
  time to fit residues: 15.2895
Evaluate side-chains
  139 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 240 ASN
B 319 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.199284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.150399 restraints weight = 9921.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.150391 restraints weight = 9979.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.151981 restraints weight = 8692.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152099 restraints weight = 6134.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.152775 restraints weight = 5925.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7964  Z= 0.136
  Angle     :  0.550   9.238  10779  Z= 0.283
  Chirality :  0.039   0.156   1160
  Planarity :  0.003   0.046   1384
  Dihedral  :  4.062  20.407   1060
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.33 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.28), residues: 940
  helix:  1.62 (0.23), residues: 504
  sheet: -1.11 (0.58), residues: 79
  loop : -1.54 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 259 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.009   0.001   PHE A 452 
 TRP   0.024   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7960)
  covalent geometry    : angle       0.54969 (10771)
  SS BOND              : bond        0.00177 (    4)
  SS BOND              : angle       0.85287 (    8)
  hydrogen bonds       : bond        0.03474 (  405)
  hydrogen bonds       : angle       4.18141 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8458 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  152 MET cc_start: 0.8885 (ttm) cc_final: 0.8530 (mtp)
REVERT: A  347 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8434 (mm)
REVERT: A  348 GLU cc_start: 0.7779 (tp30) cc_final: 0.7443 (tp30)
REVERT: A  380 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7962 (m-10)
REVERT: A  390 ASN cc_start: 0.8754 (m-40) cc_final: 0.8422 (t0)
REVERT: A  428 ASN cc_start: 0.7262 (m110) cc_final: 0.6603 (t0)
REVERT: A  444 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7894 (tp40)
REVERT: A  478 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9225 (mm)
REVERT: A  611 ASN cc_start: 0.7486 (t0) cc_final: 0.7247 (m-40)
REVERT: A  639 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8286 (tt0)
REVERT: B   64 MET cc_start: 0.8993 (mmt) cc_final: 0.8765 (mmp)
REVERT: B  216 SER cc_start: 0.2341 (OUTLIER) cc_final: 0.1397 (t)
REVERT: B  278 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: B  287 TYR cc_start: 0.9187 (m-80) cc_final: 0.8913 (m-80)
REVERT: B  353 GLU cc_start: 0.8108 (mp0) cc_final: 0.7795 (pt0)
REVERT: B  396 LYS cc_start: 0.4344 (pttt) cc_final: 0.4095 (pttt)
  outliers start: 32
  outliers final: 23
  residues processed: 139
  average time/residue: 0.0735
  time to fit residues: 14.8810
Evaluate side-chains
  139 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.199198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.150614 restraints weight = 9899.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.149108 restraints weight = 10198.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.151157 restraints weight = 9284.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.151499 restraints weight = 6298.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.151600 restraints weight = 6004.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7964  Z= 0.136
  Angle     :  0.548   9.019  10779  Z= 0.282
  Chirality :  0.039   0.154   1160
  Planarity :  0.003   0.046   1384
  Dihedral  :  4.044  20.201   1060
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.05 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.28), residues: 940
  helix:  1.59 (0.23), residues: 506
  sheet: -1.06 (0.58), residues: 79
  loop : -1.57 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.009   0.001   TYR A 368 
 PHE   0.009   0.001   PHE A 452 
 TRP   0.023   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7960)
  covalent geometry    : angle       0.54816 (10771)
  SS BOND              : bond        0.00179 (    4)
  SS BOND              : angle       0.88978 (    8)
  hydrogen bonds       : bond        0.03441 (  405)
  hydrogen bonds       : angle       4.18654 ( 1206)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.8438 (m-30) cc_final: 0.8208 (m-30)
REVERT: A  152 MET cc_start: 0.8908 (ttm) cc_final: 0.8551 (mtp)
REVERT: A  347 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8402 (mm)
REVERT: A  348 GLU cc_start: 0.7796 (tp30) cc_final: 0.7473 (tp30)
REVERT: A  380 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7946 (m-10)
REVERT: A  390 ASN cc_start: 0.8765 (m-40) cc_final: 0.8447 (t0)
REVERT: A  428 ASN cc_start: 0.7277 (m110) cc_final: 0.6682 (t0)
REVERT: A  444 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7884 (tp40)
REVERT: A  478 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9222 (mm)
REVERT: A  611 ASN cc_start: 0.7538 (t0) cc_final: 0.7315 (m-40)
REVERT: A  639 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8291 (tt0)
REVERT: B   64 MET cc_start: 0.8990 (mmt) cc_final: 0.8754 (mmp)
REVERT: B  216 SER cc_start: 0.2211 (OUTLIER) cc_final: 0.1280 (t)
REVERT: B  278 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: B  287 TYR cc_start: 0.9202 (m-80) cc_final: 0.8962 (m-80)
REVERT: B  353 GLU cc_start: 0.8085 (mp0) cc_final: 0.7796 (pt0)
  outliers start: 28
  outliers final: 22
  residues processed: 136
  average time/residue: 0.0745
  time to fit residues: 14.5241
Evaluate side-chains
  137 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  319 GLN
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 319 GLN
B 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.194942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.146549 restraints weight = 9857.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.144787 restraints weight = 11563.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.147048 restraints weight = 10183.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.147121 restraints weight = 7139.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.147484 restraints weight = 7198.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7964  Z= 0.126
  Angle     :  0.551   8.977  10779  Z= 0.283
  Chirality :  0.039   0.153   1160
  Planarity :  0.003   0.046   1384
  Dihedral  :  4.015  19.976   1060
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.52 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.27), residues: 940
  helix:  1.62 (0.23), residues: 506
  sheet: -1.01 (0.58), residues: 79
  loop : -1.65 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 259 
 TYR   0.011   0.001   TYR A 368 
 PHE   0.008   0.001   PHE A 452 
 TRP   0.022   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7960)
  covalent geometry    : angle       0.55076 (10771)
  SS BOND              : bond        0.00175 (    4)
  SS BOND              : angle       0.81350 (    8)
  hydrogen bonds       : bond        0.03355 (  405)
  hydrogen bonds       : angle       4.17707 ( 1206)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1142.64 seconds
wall clock time: 20 minutes 29.13 seconds (1229.13 seconds total)