Starting phenix.real_space_refine
on Wed Sep 17 09:10:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l1s_62753/09_2025/9l1s_62753.cif"
  }
  resolution = 3.0
  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=   0.004
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      60      5.16       5
     C    4742      2.51       5
     N    1319      2.21       5
     O    1463      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7584
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 553, 4266
          Classifications: {'peptide': 553}
          Link IDs: {'PTRANS': 33, 'TRANS': 519}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1657
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202}
    Chain: "C"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1661
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 208}
  Time building chain proxies: 1.97, per 1000 atoms: 0.26
  Number of scatterers: 7584
  At special positions: 0
  Unit cell: (89.232, 113.568, 140.946, 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      60     16.00
     O    1463      8.00
     N    1319      7.00
     C    4742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 475 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 544 " - pdb=" SG  CYS A 560 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 140 " - pdb=" SG  CYS C 196 " distance=2.03

  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: 0.58
  Conformation dependent library (CDL) restraints added in 463.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 22 sheets defined
      7.0% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 48
      removed outlier: 3.649A  pdb=" N   HIS A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
      removed outlier: 3.608A  pdb=" N   GLN A  75 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
      removed outlier: 3.688A  pdb=" N   ASP A 110 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 4.263A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 4.231A  pdb=" N   CYS A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 395 through 401
      removed outlier: 3.781A  pdb=" N   GLN A 398 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A 399 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 400 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.788A  pdb=" N   GLY A 518 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 187
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.654A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 158
      No H-bonds generated for 'chain 'C' and resid 156 through 158'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 3.575A  pdb=" N   CYS A  26 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 3.552A  pdb=" N   TYR A  64 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ASN A  89 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A 183 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260
      removed outlier: 3.521A  pdb=" N   PHE A 258 " --> pdb=" O   GLU A 265 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 274
    Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 323
    Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 343
      removed outlier: 6.517A  pdb=" N   CYS A 342 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 376
      removed outlier: 7.451A  pdb=" N   LEU A 467 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   THR A 444 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   HIS A 469 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLN A 446 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 406
    Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 541
      removed outlier: 3.578A  pdb=" N   GLU A 539 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 534 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU A 535 " --> pdb=" O   CYS A 560 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 552 through 553
    Processing sheet with id=AB4, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.634A  pdb=" N   THR B  74 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 13
    Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 54
      removed outlier: 5.828A  pdb=" N   LEU B  46 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLN B  37 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE B  48 " --> pdb=" O   TRP B  35 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 129 through 133
    Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 150
      removed outlier: 3.511A  pdb=" N   LYS B 145 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS B 194 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LYS B 207 " --> pdb=" O   CYS B 194 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 5 through 7
    Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.043A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 110 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR C 107 " --> pdb=" O   TYR C  90 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   MET C  34 " --> pdb=" O   ASP C  50 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   ASP C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 122 through 124
      removed outlier: 3.691A  pdb=" N   GLY C 139 " --> pdb=" O   LEU C 124 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER C 180 " --> pdb=" O   CYS C 140 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 154
      removed outlier: 4.379A  pdb=" N   TYR C 194 " --> pdb=" O   VAL C 211 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS C 209 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170

    140 hydrogen bonds defined for protein.
    333 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: 1.22

  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: 2518
        1.34 -     1.46: 1691
        1.46 -     1.58: 3483
        1.58 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 7760
  Sorted by residual:
  bond pdb=" N   LEU A 509 "
       pdb=" CA  LEU A 509 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 1.46e-02 4.69e+03 3.42e+00
  bond pdb=" C   ARG A  34 "
       pdb=" N   LEU A  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.352 -0.022 1.47e-02 4.63e+03 2.20e+00
  bond pdb=" N   ASN C 155 "
       pdb=" CA  ASN C 155 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.51e+00
  bond pdb=" C   LEU A 509 "
       pdb=" O   LEU A 509 "
    ideal  model  delta    sigma   weight residual
    1.232  1.246 -0.014 1.20e-02 6.94e+03 1.38e+00
  bond pdb=" CA  CYS A 511 "
       pdb=" C   CYS A 511 "
    ideal  model  delta    sigma   weight residual
    1.532  1.521  0.011 9.60e-03 1.09e+04 1.33e+00
  ... (remaining 7755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10237
        1.67 -     3.34: 273
        3.34 -     5.01: 35
        5.01 -     6.69: 4
        6.69 -     8.36: 6
  Bond angle restraints: 10555
  Sorted by residual:
  angle pdb=" N   VAL A 219 "
        pdb=" CA  VAL A 219 "
        pdb=" C   VAL A 219 "
      ideal   model   delta    sigma   weight residual
     113.20  108.50    4.70 9.60e-01 1.09e+00 2.39e+01
  angle pdb=" C   SER A 451 "
        pdb=" N   TRP A 452 "
        pdb=" CA  TRP A 452 "
      ideal   model   delta    sigma   weight residual
     121.90  116.10    5.80 1.26e+00 6.30e-01 2.12e+01
  angle pdb=" C   ARG A  34 "
        pdb=" N   LEU A  35 "
        pdb=" CA  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     120.68  127.43   -6.75 1.52e+00 4.33e-01 1.97e+01
  angle pdb=" C   ASN A 275 "
        pdb=" N   THR A 276 "
        pdb=" CA  THR A 276 "
      ideal   model   delta    sigma   weight residual
     121.54  128.25   -6.71 1.91e+00 2.74e-01 1.24e+01
  angle pdb=" N   GLY C  97 "
        pdb=" CA  GLY C  97 "
        pdb=" C   GLY C  97 "
      ideal   model   delta    sigma   weight residual
     112.34  105.53    6.81 2.04e+00 2.40e-01 1.11e+01
  ... (remaining 10550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4291
       17.96 -    35.92: 312
       35.92 -    53.88: 57
       53.88 -    71.84: 22
       71.84 -    89.80: 15
  Dihedral angle restraints: 4697
    sinusoidal: 1854
      harmonic: 2843
  Sorted by residual:
  dihedral pdb=" CA  MET A 347 "
           pdb=" C   MET A 347 "
           pdb=" N   GLU A 348 "
           pdb=" CA  GLU A 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.63  -25.37     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  PRO C  98 "
           pdb=" C   PRO C  98 "
           pdb=" N   SER C  99 "
           pdb=" CA  SER C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.27   22.73     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.34   37.66     1      1.00e+01 1.00e-02 2.00e+01
  ... (remaining 4694 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 838
       0.043 -    0.086: 260
       0.086 -    0.129: 70
       0.129 -    0.172: 5
       0.172 -    0.216: 1
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  LEU A 509 "
            pdb=" N   LEU A 509 "
            pdb=" C   LEU A 509 "
            pdb=" CB  LEU A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  VAL A 314 "
            pdb=" N   VAL A 314 "
            pdb=" C   VAL A 314 "
            pdb=" CB  VAL A 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.59e-01
  chirality pdb=" CG  LEU A 535 "
            pdb=" CB  LEU A 535 "
            pdb=" CD1 LEU A 535 "
            pdb=" CD2 LEU A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1383
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  79 "    0.088 5.00e-02 4.00e+02   1.34e-01 2.87e+01
        pdb=" N   PRO B  80 "   -0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 118 "    0.068 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO B 119 "   -0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO B 119 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO B 119 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 246 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO A 247 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 247 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 247 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1380 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 39
        2.54 -     3.13: 5514
        3.13 -     3.72: 11225
        3.72 -     4.31: 16019
        4.31 -     4.90: 26919
  Nonbonded interactions: 59716
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 504 "
            pdb=" CD1 LEU A 509 "
     model   vdw
     1.945 3.460
  nonbonded pdb=" OH  TYR A 301 "
            pdb=" OE2 GLU A 460 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG1 THR A 290 "
            pdb=" O   GLY A 309 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   PRO A 420 "
            pdb=" N   SER A 451 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OE2 GLU A 321 "
            pdb=" NE2 GLN A 329 "
     model   vdw
     2.280 3.120
  ... (remaining 59711 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 individual isotropic
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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
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      :  0.003   0.054   7781  Z= 0.132
  Angle     :  0.657   8.356  10597  Z= 0.370
  Chirality :  0.044   0.216   1174
  Planarity :  0.006   0.134   1383
  Dihedral  : 14.050  89.804   2814
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.35 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.26), residues: 981
  helix: -3.77 (0.60), residues: 38
  sheet: -1.37 (0.33), residues: 253
  loop : -1.33 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 143 
 TYR   0.012   0.001   TYR A  64 
 PHE   0.013   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.007   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7760)
  covalent geometry    : angle       0.65554 (10555)
  SS BOND              : bond        0.00190 (   21)
  SS BOND              : angle       0.97131 (   42)
  hydrogen bonds       : bond        0.28712 (  140)
  hydrogen bonds       : angle      10.99563 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  554 TYR cc_start: 0.6348 (p90) cc_final: 0.6044 (p90)
REVERT: B  137 ASN cc_start: 0.7723 (t0) cc_final: 0.7369 (t160)
  outliers start: 2
  outliers final: 2
  residues processed: 129
  average time/residue: 0.5871
  time to fit residues: 79.9219
Evaluate side-chains
  80 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  488 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   30.0000
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
A 176 ASN
A 239 GLN
A 473 HIS
B 199 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.165652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.123972 restraints weight = 9961.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 3.03
r_work: 0.3600 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7781  Z= 0.145
  Angle     :  0.672   8.818  10597  Z= 0.346
  Chirality :  0.046   0.258   1174
  Planarity :  0.006   0.095   1383
  Dihedral  :  4.921  24.256   1071
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.03 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.94 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.26), residues: 981
  helix: -3.70 (0.61), residues: 38
  sheet: -1.11 (0.32), residues: 249
  loop : -1.22 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  62 
 TYR   0.010   0.001   TYR B  94 
 PHE   0.020   0.002   PHE A 534 
 TRP   0.010   0.002   TRP A 205 
 HIS   0.010   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7760)
  covalent geometry    : angle       0.66272 (10555)
  SS BOND              : bond        0.00466 (   21)
  SS BOND              : angle       1.85846 (   42)
  hydrogen bonds       : bond        0.03785 (  140)
  hydrogen bonds       : angle       7.23281 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  554 TYR cc_start: 0.6620 (p90) cc_final: 0.6168 (p90)
REVERT: B  147 GLN cc_start: 0.7965 (pm20) cc_final: 0.7705 (pm20)
REVERT: C    3 GLN cc_start: 0.7848 (pp30) cc_final: 0.7567 (pp30)
REVERT: C   82 MET cc_start: 0.7744 (mtm) cc_final: 0.7530 (mtp)
REVERT: C  102 TYR cc_start: 0.7847 (m-80) cc_final: 0.7625 (m-80)
  outliers start: 18
  outliers final: 7
  residues processed: 107
  average time/residue: 0.5457
  time to fit residues: 62.0003
Evaluate side-chains
  91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  541 VAL
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0050
   chunk 68 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 23 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
A 176 ASN
A 239 GLN
A 275 ASN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.167919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.122334 restraints weight = 9977.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.56
r_work: 0.3654 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7781  Z= 0.108
  Angle     :  0.613   9.566  10597  Z= 0.315
  Chirality :  0.044   0.156   1174
  Planarity :  0.005   0.074   1383
  Dihedral  :  4.695  23.292   1067
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.53 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.26), residues: 981
  helix: -3.89 (0.55), residues: 38
  sheet: -0.85 (0.33), residues: 238
  loop : -1.20 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  62 
 TYR   0.008   0.001   TYR C  99B
 PHE   0.014   0.001   PHE A  73 
 TRP   0.012   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7760)
  covalent geometry    : angle       0.60959 (10555)
  SS BOND              : bond        0.00274 (   21)
  SS BOND              : angle       1.25144 (   42)
  hydrogen bonds       : bond        0.02998 (  140)
  hydrogen bonds       : angle       6.40029 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  275 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7726 (t0)
REVERT: A  554 TYR cc_start: 0.6813 (p90) cc_final: 0.6483 (p90)
REVERT: B  147 GLN cc_start: 0.8059 (pm20) cc_final: 0.7849 (pm20)
REVERT: B  189 HIS cc_start: 0.7226 (m90) cc_final: 0.6916 (m-70)
REVERT: B  199 GLN cc_start: 0.8948 (tt0) cc_final: 0.8620 (tm130)
REVERT: C    3 GLN cc_start: 0.7830 (pp30) cc_final: 0.7492 (pp30)
REVERT: C  102 TYR cc_start: 0.7774 (m-80) cc_final: 0.7547 (m-80)
REVERT: C  195 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6782 (mp)
  outliers start: 17
  outliers final: 8
  residues processed: 106
  average time/residue: 0.4886
  time to fit residues: 55.4650
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  275 ASN
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A  93 GLN
A 512 HIS
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.162599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.116395 restraints weight = 10178.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.53
r_work: 0.3572 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7781  Z= 0.175
  Angle     :  0.683   9.408  10597  Z= 0.348
  Chirality :  0.046   0.154   1174
  Planarity :  0.005   0.062   1383
  Dihedral  :  5.040  24.316   1067
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.53 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.26), residues: 981
  helix: -3.67 (0.62), residues: 38
  sheet: -0.94 (0.32), residues: 262
  loop : -1.19 (0.23), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  18 
 TYR   0.016   0.002   TYR B  94 
 PHE   0.016   0.002   PHE A  73 
 TRP   0.016   0.002   TRP A 169 
 HIS   0.005   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7760)
  covalent geometry    : angle       0.67965 (10555)
  SS BOND              : bond        0.00310 (   21)
  SS BOND              : angle       1.25480 (   42)
  hydrogen bonds       : bond        0.03292 (  140)
  hydrogen bonds       : angle       6.41223 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  509 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4308 (pp)
REVERT: B  147 GLN cc_start: 0.8045 (pm20) cc_final: 0.7699 (pm20)
REVERT: B  199 GLN cc_start: 0.8954 (tt0) cc_final: 0.8534 (tm-30)
REVERT: C    3 GLN cc_start: 0.7999 (pp30) cc_final: 0.7555 (pp30)
REVERT: C   46 GLU cc_start: 0.7669 (tt0) cc_final: 0.7415 (tt0)
REVERT: C   85 GLU cc_start: 0.7924 (tp30) cc_final: 0.7720 (tp30)
REVERT: C  102 TYR cc_start: 0.7958 (m-80) cc_final: 0.7705 (m-80)
REVERT: C  195 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6656 (mm)
  outliers start: 20
  outliers final: 12
  residues processed: 101
  average time/residue: 0.5280
  time to fit residues: 56.9682
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  541 VAL
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  144 ASP
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0020
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
B 137 ASN
** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.167652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.121236 restraints weight = 10116.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.69
r_work: 0.3628 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7781  Z= 0.103
  Angle     :  0.610   8.274  10597  Z= 0.311
  Chirality :  0.044   0.139   1174
  Planarity :  0.005   0.055   1383
  Dihedral  :  4.672  23.983   1067
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.00 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.26), residues: 981
  helix: -3.32 (0.65), residues: 38
  sheet: -0.60 (0.33), residues: 247
  loop : -1.09 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  18 
 TYR   0.011   0.001   TYR C  90 
 PHE   0.016   0.001   PHE A  73 
 TRP   0.018   0.001   TRP A 169 
 HIS   0.004   0.000   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7760)
  covalent geometry    : angle       0.60888 (10555)
  SS BOND              : bond        0.00285 (   21)
  SS BOND              : angle       0.89375 (   42)
  hydrogen bonds       : bond        0.02613 (  140)
  hydrogen bonds       : angle       5.85727 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7487 (t) cc_final: 0.7220 (p)
REVERT: A  509 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.3853 (pp)
REVERT: A  533 GLN cc_start: 0.8966 (mp10) cc_final: 0.8299 (mp10)
REVERT: B  199 GLN cc_start: 0.8977 (tt0) cc_final: 0.8526 (tm130)
REVERT: C    3 GLN cc_start: 0.7888 (pp30) cc_final: 0.7459 (pp30)
REVERT: C   62 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7836 (ttp-110)
REVERT: C   85 GLU cc_start: 0.7883 (tp30) cc_final: 0.7573 (tp30)
REVERT: C  102 TYR cc_start: 0.7837 (m-80) cc_final: 0.7580 (m-80)
REVERT: C  142 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8389 (p)
REVERT: C  195 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6777 (mm)
  outliers start: 16
  outliers final: 10
  residues processed: 106
  average time/residue: 0.5021
  time to fit residues: 56.9066
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  541 VAL
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 20 optimal weight:    0.4980
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
B 137 ASN
** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.165906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119337 restraints weight = 10155.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.68
r_work: 0.3610 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7781  Z= 0.123
  Angle     :  0.630   8.886  10597  Z= 0.319
  Chirality :  0.044   0.137   1174
  Planarity :  0.005   0.051   1383
  Dihedral  :  4.671  24.101   1067
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.88 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.26), residues: 981
  helix: -2.94 (0.72), residues: 38
  sheet: -0.56 (0.34), residues: 247
  loop : -1.03 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 108 
 TYR   0.017   0.001   TYR B 140 
 PHE   0.020   0.001   PHE C 122 
 TRP   0.020   0.001   TRP A 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7760)
  covalent geometry    : angle       0.62795 (10555)
  SS BOND              : bond        0.00263 (   21)
  SS BOND              : angle       0.95277 (   42)
  hydrogen bonds       : bond        0.02670 (  140)
  hydrogen bonds       : angle       5.85359 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7608 (t) cc_final: 0.7314 (p)
REVERT: B  145 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8379 (ptmm)
REVERT: B  147 GLN cc_start: 0.8068 (pm20) cc_final: 0.7784 (pm20)
REVERT: B  189 HIS cc_start: 0.7358 (m90) cc_final: 0.7123 (m90)
REVERT: B  199 GLN cc_start: 0.8971 (tt0) cc_final: 0.8526 (tm-30)
REVERT: C    3 GLN cc_start: 0.7972 (pp30) cc_final: 0.7465 (pp30)
REVERT: C   62 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7971 (ttp-110)
REVERT: C   85 GLU cc_start: 0.7944 (tp30) cc_final: 0.7649 (tp30)
REVERT: C  102 TYR cc_start: 0.7908 (m-80) cc_final: 0.7661 (m-80)
REVERT: C  195 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6696 (mm)
  outliers start: 25
  outliers final: 9
  residues processed: 102
  average time/residue: 0.4492
  time to fit residues: 49.4086
Evaluate side-chains
  87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 71 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN
B  27 GLN
B 137 ASN
B 160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.166587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.120174 restraints weight = 10097.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.68
r_work: 0.3622 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7781  Z= 0.116
  Angle     :  0.626   8.699  10597  Z= 0.316
  Chirality :  0.044   0.136   1174
  Planarity :  0.004   0.050   1383
  Dihedral  :  4.622  23.798   1067
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.71 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.27), residues: 981
  helix: -2.64 (0.79), residues: 38
  sheet: -0.50 (0.34), residues: 247
  loop : -0.98 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 108 
 TYR   0.009   0.001   TYR C  90 
 PHE   0.019   0.001   PHE A  73 
 TRP   0.024   0.001   TRP A 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7760)
  covalent geometry    : angle       0.62417 (10555)
  SS BOND              : bond        0.00218 (   21)
  SS BOND              : angle       0.93873 (   42)
  hydrogen bonds       : bond        0.02521 (  140)
  hydrogen bonds       : angle       5.65458 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   94 VAL cc_start: 0.7593 (t) cc_final: 0.7313 (p)
REVERT: A  509 LEU cc_start: 0.4351 (OUTLIER) cc_final: 0.3696 (pp)
REVERT: B  145 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8388 (ptmm)
REVERT: B  147 GLN cc_start: 0.8070 (pm20) cc_final: 0.7811 (pm20)
REVERT: B  189 HIS cc_start: 0.7266 (m90) cc_final: 0.7064 (m90)
REVERT: B  199 GLN cc_start: 0.8956 (tt0) cc_final: 0.8522 (tm-30)
REVERT: C    3 GLN cc_start: 0.7962 (pp30) cc_final: 0.7622 (pp30)
REVERT: C   34 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7074 (mmm)
REVERT: C   85 GLU cc_start: 0.7965 (tp30) cc_final: 0.7602 (tp30)
REVERT: C  102 TYR cc_start: 0.7928 (m-80) cc_final: 0.7672 (m-80)
REVERT: C  117 LYS cc_start: 0.8753 (mtpm) cc_final: 0.7313 (mtpp)
REVERT: C  144 ASP cc_start: 0.7722 (m-30) cc_final: 0.7296 (t0)
REVERT: C  195 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6757 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 100
  average time/residue: 0.4678
  time to fit residues: 50.2217
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 82 optimal weight:    0.4980
   chunk 18 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0970
   chunk 83 optimal weight:    0.8980
   chunk 89 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
B 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.163102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.117171 restraints weight = 10234.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.53
r_work: 0.3578 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7781  Z= 0.153
  Angle     :  0.669   9.473  10597  Z= 0.336
  Chirality :  0.045   0.141   1174
  Planarity :  0.005   0.049   1383
  Dihedral  :  4.841  23.930   1067
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.06 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.26), residues: 981
  helix: -2.56 (0.83), residues: 38
  sheet: -0.40 (0.34), residues: 238
  loop : -1.06 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 108 
 TYR   0.014   0.001   TYR B  94 
 PHE   0.021   0.001   PHE A  73 
 TRP   0.025   0.002   TRP A 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7760)
  covalent geometry    : angle       0.66657 (10555)
  SS BOND              : bond        0.00272 (   21)
  SS BOND              : angle       1.05772 (   42)
  hydrogen bonds       : bond        0.02764 (  140)
  hydrogen bonds       : angle       5.78117 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7416 (t) cc_final: 0.7166 (p)
REVERT: B  145 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8394 (ptmm)
REVERT: B  147 GLN cc_start: 0.8144 (pm20) cc_final: 0.7868 (pm20)
REVERT: B  199 GLN cc_start: 0.8948 (tt0) cc_final: 0.8481 (tm-30)
REVERT: C    3 GLN cc_start: 0.8042 (pp30) cc_final: 0.7718 (pp30)
REVERT: C   34 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7178 (mmm)
REVERT: C   85 GLU cc_start: 0.7983 (tp30) cc_final: 0.7778 (tp30)
REVERT: C  102 TYR cc_start: 0.7964 (m-80) cc_final: 0.7701 (m-80)
REVERT: C  117 LYS cc_start: 0.8812 (mtpm) cc_final: 0.7752 (mtpp)
REVERT: C  144 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7280 (t0)
REVERT: C  195 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6699 (mm)
  outliers start: 19
  outliers final: 11
  residues processed: 99
  average time/residue: 0.4492
  time to fit residues: 47.7349
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  144 ASP
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 66 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0030
   chunk 76 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN
B 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.166850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.121204 restraints weight = 10085.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.62
r_work: 0.3641 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7781  Z= 0.110
  Angle     :  0.639  10.021  10597  Z= 0.319
  Chirality :  0.044   0.142   1174
  Planarity :  0.004   0.051   1383
  Dihedral  :  4.596  23.944   1067
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.29 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.27), residues: 981
  helix: -2.43 (0.84), residues: 38
  sheet: -0.35 (0.35), residues: 238
  loop : -1.00 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 108 
 TYR   0.009   0.001   TYR C  90 
 PHE   0.024   0.001   PHE A 534 
 TRP   0.017   0.001   TRP A 169 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7760)
  covalent geometry    : angle       0.63756 (10555)
  SS BOND              : bond        0.00203 (   21)
  SS BOND              : angle       0.84890 (   42)
  hydrogen bonds       : bond        0.02439 (  140)
  hydrogen bonds       : angle       5.48541 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7484 (t) cc_final: 0.7236 (p)
REVERT: B  145 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8283 (ptmm)
REVERT: C    3 GLN cc_start: 0.7980 (pp30) cc_final: 0.7616 (pp30)
REVERT: C   64 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8087 (ttmp)
REVERT: C   85 GLU cc_start: 0.7942 (tp30) cc_final: 0.7688 (tp30)
REVERT: C  102 TYR cc_start: 0.7808 (m-80) cc_final: 0.7585 (m-80)
REVERT: C  117 LYS cc_start: 0.8799 (mtpm) cc_final: 0.7785 (mtpp)
REVERT: C  144 ASP cc_start: 0.7587 (m-30) cc_final: 0.7243 (t0)
REVERT: C  195 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6758 (mm)
  outliers start: 19
  outliers final: 11
  residues processed: 105
  average time/residue: 0.4856
  time to fit residues: 54.3518
Evaluate side-chains
  93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.1980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  97 GLN
B 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.166125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.125683 restraints weight = 10104.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 3.00
r_work: 0.3622 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7781  Z= 0.119
  Angle     :  0.659  10.489  10597  Z= 0.327
  Chirality :  0.044   0.141   1174
  Planarity :  0.005   0.063   1383
  Dihedral  :  4.624  24.353   1067
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.12 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.27), residues: 981
  helix: -2.45 (0.82), residues: 38
  sheet: -0.34 (0.34), residues: 238
  loop : -0.98 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.011   0.001   TYR C  99B
 PHE   0.024   0.001   PHE A 534 
 TRP   0.027   0.002   TRP A 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7760)
  covalent geometry    : angle       0.65836 (10555)
  SS BOND              : bond        0.00202 (   21)
  SS BOND              : angle       0.86735 (   42)
  hydrogen bonds       : bond        0.02490 (  140)
  hydrogen bonds       : angle       5.50433 (  333)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7541 (t) cc_final: 0.7292 (p)
REVERT: A  509 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4144 (pp)
REVERT: B  137 ASN cc_start: 0.8479 (t0) cc_final: 0.8132 (t160)
REVERT: C    3 GLN cc_start: 0.8021 (pp30) cc_final: 0.7682 (pp30)
REVERT: C   64 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8090 (ttmp)
REVERT: C   85 GLU cc_start: 0.7977 (tp30) cc_final: 0.7739 (tp30)
REVERT: C  102 TYR cc_start: 0.7878 (m-80) cc_final: 0.7664 (m-80)
REVERT: C  117 LYS cc_start: 0.8787 (mtpm) cc_final: 0.7805 (mtpp)
REVERT: C  195 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6754 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 95
  average time/residue: 0.4411
  time to fit residues: 45.0150
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 92 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN
B 166 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.162902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.116704 restraints weight = 10068.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.53
r_work: 0.3579 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7781  Z= 0.176
  Angle     :  0.715  10.329  10597  Z= 0.356
  Chirality :  0.046   0.174   1174
  Planarity :  0.005   0.055   1383
  Dihedral  :  4.937  24.566   1067
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.88 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.26), residues: 981
  helix: -2.59 (0.81), residues: 38
  sheet: -0.37 (0.34), residues: 240
  loop : -1.09 (0.23), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.016   0.002   TYR B  94 
 PHE   0.024   0.002   PHE A 534 
 TRP   0.035   0.002   TRP A 169 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7760)
  covalent geometry    : angle       0.71302 (10555)
  SS BOND              : bond        0.00266 (   21)
  SS BOND              : angle       1.07275 (   42)
  hydrogen bonds       : bond        0.02928 (  140)
  hydrogen bonds       : angle       5.77737 (  333)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3893.30 seconds
wall clock time: 66 minutes 59.46 seconds (4019.46 seconds total)