Starting phenix.real_space_refine
on Thu Mar  6 02:43:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgf_22325/03_2025/7jgf_22325.cif"
  }
  resolution = 4.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2808      2.51       5
     N     770      2.21       5
     O     839      1.98       5
     H      30      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4477
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4477
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 532, 4455
          Classifications: {'peptide': 532}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 15, 'TRANS': 516}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 532, 4455
          Classifications: {'peptide': 532}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 15, 'TRANS': 516}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 4528
      Conformer: "C"
        Number of residues, atoms: 532, 4439
          Classifications: {'peptide': 532}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 15, 'TRANS': 516}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
          bond proxies already assigned to first conformer: 4528
  Time building chain proxies: 10.43, per 1000 atoms: 2.33
  Number of scatterers: 4477
  At special positions: 0
  Unit cell: (74.06, 137.54, 93.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     O     839      8.00
     N     770      7.00
     C    2808      6.00
     H      30      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2208 " - pdb=" SG  CYS A2224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2331 " - pdb=" SG  CYS A2478 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2516 " - pdb=" SG  CYS A2599 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2530 " - pdb=" SG  CYS A2545 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2592 " - pdb=" SG  CYS A2597 " 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: 1.07
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1024

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      65.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2023 through 2032
    Processing helix  chain 'A' and resid 2060 through 2086
      removed outlier: 4.283A  pdb=" N   LEU A2079 " --> pdb=" O   GLU A2075 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY A2080 " --> pdb=" O   GLY A2076 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN A2081 " --> pdb=" O   LYS A2077 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LYS A2084 " --> pdb=" O   GLY A2080 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLU A2085 " --> pdb=" O   ASN A2081 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS A2086 " --> pdb=" O   TYR A2082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2088 through 2110
      removed outlier: 3.977A  pdb=" N   TYR A2103 " --> pdb=" O   SER A2099 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   GLU A2104 " --> pdb=" O   PHE A2100 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ASP A2105 " --> pdb=" O   TYR A2101 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ILE A2106 " --> pdb=" O   ASP A2102 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE A2107 " --> pdb=" O   TYR A2103 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A2110 " --> pdb=" O   ILE A2106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2117 through 2130
      removed outlier: 3.627A  pdb=" N   LYS A2122 " --> pdb=" O   PHE A2118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2135 through 2157
      removed outlier: 3.574A  pdb=" N   TRP A2143 " --> pdb=" O   ALA A2139 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LYS A2148 " --> pdb=" O   LYS A2144 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   SER A2149 " --> pdb=" O   THR A2145 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   TRP A2151 " --> pdb=" O   LYS A2147 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   MET A2154 " --> pdb=" O   ILE A2150 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A2155 " --> pdb=" O   TRP A2151 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   CYS A2156 " --> pdb=" O   ASN A2152 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLY A2157 " --> pdb=" O   ALA A2153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2183 through 2207
    Processing helix  chain 'A' and resid 2221 through 2252
      removed outlier: 3.599A  pdb=" N   ILE A2240 " --> pdb=" O   ARG A2236 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ARG A2241 " --> pdb=" O   LYS A2237 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TRP A2242 " --> pdb=" O   ARG A2238 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU A2243 " --> pdb=" O   SER A2239 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A2244 " --> pdb=" O   ILE A2240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2294 through 2300
      removed outlier: 4.137A  pdb=" N   PHE A2298 " --> pdb=" O   GLU A2294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2302 through 2310
      removed outlier: 3.860A  pdb=" N   ILE A2307 " --> pdb=" O   GLN A2304 " (cutoff:3.500A)
      Proline residue:  A2308  - end of helix
    Processing helix  chain 'A' and resid 2328 through 2337
      removed outlier: 3.849A  pdb=" N   LYS A2333 " --> pdb=" O   TYR A2329 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   TYR A2334 " --> pdb=" O   ILE A2330 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS A2335 " --> pdb=" O   CYS A2331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2367 through 2372
      removed outlier: 4.344A  pdb=" N   ASN A2372 " --> pdb=" O   PRO A2368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2378 through 2380
      No H-bonds generated for 'chain 'A' and resid 2378 through 2380'
    Processing helix  chain 'A' and resid 2381 through 2388
      removed outlier: 3.527A  pdb=" N   TYR A2385 " --> pdb=" O   LYS A2381 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS A2386 " --> pdb=" O   ILE A2382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2388 through 2411
      removed outlier: 3.975A  pdb=" N   PHE A2392 " --> pdb=" O   ASP A2388 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP A2394 " --> pdb=" O   LYS A2390 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   LYS A2408 " --> pdb=" O   VAL A2404 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LYS A2409 " --> pdb=" O   GLU A2405 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA A2410 " --> pdb=" O   ARG A2406 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   TYR A2411 " --> pdb=" O   LEU A2407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2414 through 2433
    Processing helix  chain 'A' and resid 2441 through 2451
    Processing helix  chain 'A' and resid 2458 through 2484
      removed outlier: 3.686A  pdb=" N   CYS A2478 " --> pdb=" O   GLU A2474 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A2484 " --> pdb=" O   TYR A2480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2496 through 2501
      removed outlier: 3.540A  pdb=" N   GLU A2499 " --> pdb=" O   PRO A2496 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A2501 " --> pdb=" O   ILE A2498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2502 through 2513
    Processing helix  chain 'A' and resid 2515 through 2529
      removed outlier: 3.726A  pdb=" N   TYR A2523 " --> pdb=" O   ARG A2519 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN A2527 " --> pdb=" O   TYR A2523 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A2528 " --> pdb=" O   ASP A2524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2546 through 2548
      No H-bonds generated for 'chain 'A' and resid 2546 through 2548'
    Processing helix  chain 'A' and resid 2549 through 2574
      removed outlier: 4.107A  pdb=" N   LYS A2553 " --> pdb=" O   CYS A2549 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASP A2571 " --> pdb=" O   THR A2567 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLU A2573 " --> pdb=" O   LYS A2569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2583 through 2591
      removed outlier: 3.894A  pdb=" N   LYS A2589 " --> pdb=" O   PRO A2585 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2166 through 2167

    210 hydrogen bonds defined for protein.
    618 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: 1.15

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 30
        1.05 -     1.24: 585
        1.24 -     1.43: 1336
        1.43 -     1.62: 2578
        1.62 -     1.81: 42
  Bond restraints: 4571
  Sorted by residual:
  bond pdb=" CA  PHE A2064 "
       pdb=" CB  PHE A2064 "
    ideal  model  delta    sigma   weight residual
    1.529  1.550 -0.021 1.74e-02 3.30e+03 1.41e+00
  bond pdb=" CG  MET A2422 "
       pdb=" SD  MET A2422 "
    ideal  model  delta    sigma   weight residual
    1.803  1.773  0.030 2.50e-02 1.60e+03 1.41e+00
  bond pdb=" CA  PHE A2574 "
       pdb=" C   PHE A2574 "
    ideal  model  delta    sigma   weight residual
    1.522  1.537 -0.014 1.51e-02 4.39e+03 9.22e-01
  bond pdb=" CB  GLU A2202 "
       pdb=" CG  GLU A2202 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.16e-01
  bond pdb=" CA  PHE A2182 "
       pdb=" C   PHE A2182 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.015 1.75e-02 3.27e+03 6.94e-01
  ... (remaining 4566 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 5904
        1.41 -     2.83: 196
        2.83 -     4.24: 30
        4.24 -     5.66: 10
        5.66 -     7.07: 3
  Bond angle restraints: 6143
  Sorted by residual:
  angle pdb=" C   ALA A2421 "
        pdb=" N   MET A2422 "
        pdb=" CA  MET A2422 "
      ideal   model   delta    sigma   weight residual
     121.14  114.07    7.07 1.75e+00 3.27e-01 1.63e+01
  angle pdb=" C   GLU A2063 "
        pdb=" N   PHE A2064 "
        pdb=" CA  PHE A2064 "
      ideal   model   delta    sigma   weight residual
     120.72  115.30    5.42 1.67e+00 3.59e-01 1.05e+01
  angle pdb=" N   MET A2422 "
        pdb=" CA  MET A2422 "
        pdb=" CB  MET A2422 "
      ideal   model   delta    sigma   weight residual
     110.40  115.64   -5.24 1.63e+00 3.76e-01 1.03e+01
  angle pdb=" N   GLY A2412 "
        pdb=" CA  GLY A2412 "
        pdb=" C   GLY A2412 "
      ideal   model   delta    sigma   weight residual
     110.20  114.32   -4.12 1.32e+00 5.74e-01 9.74e+00
  angle pdb=" CA  MET A2422 "
        pdb=" CB  MET A2422 "
        pdb=" CG  MET A2422 "
      ideal   model   delta    sigma   weight residual
     114.10  119.70   -5.60 2.00e+00 2.50e-01 7.83e+00
  ... (remaining 6138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2550
       17.85 -    35.70: 223
       35.70 -    53.55: 37
       53.55 -    71.39: 5
       71.39 -    89.24: 3
  Dihedral angle restraints: 2818
    sinusoidal: 1240
      harmonic: 1578
  Sorted by residual:
  dihedral pdb=" CB  CYS A2208 "
           pdb=" SG  CYS A2208 "
           pdb=" SG  CYS A2224 "
           pdb=" CB  CYS A2224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    3.24  -89.24     1      1.00e+01 1.00e-02 9.47e+01
  dihedral pdb=" CB  CYS A2516 "
           pdb=" SG  CYS A2516 "
           pdb=" SG  CYS A2599 "
           pdb=" CB  CYS A2599 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -14.43  -71.57     1      1.00e+01 1.00e-02 6.57e+01
  dihedral pdb=" CB  CYS A2530 "
           pdb=" SG  CYS A2530 "
           pdb=" SG  CYS A2545 "
           pdb=" CB  CYS A2545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.56  -32.44     1      1.00e+01 1.00e-02 1.50e+01
  ... (remaining 2815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 409
       0.033 -    0.065: 153
       0.065 -    0.097: 43
       0.097 -    0.130: 12
       0.130 -    0.162: 3
  Chirality restraints: 620
  Sorted by residual:
  chirality pdb=" CA  PHE A2064 "
            pdb=" N   PHE A2064 "
            pdb=" C   PHE A2064 "
            pdb=" CB  PHE A2064 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" CG  LEU A2113 "
            pdb=" CB  LEU A2113 "
            pdb=" CD1 LEU A2113 "
            pdb=" CD2 LEU A2113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CB  VAL A2404 "
            pdb=" CA  VAL A2404 "
            pdb=" CG1 VAL A2404 "
            pdb=" CG2 VAL A2404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 617 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A2234 "    0.022 2.00e-02 2.50e+03   2.20e-02 1.21e+01
        pdb=" CG  TRP A2234 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A2234 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A2234 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A2234 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A2234 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A2234 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A2234 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A2234 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A2234 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A2495 "   -0.045 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO A2496 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A2496 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A2496 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A2584 "   -0.039 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A2585 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A2585 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A2585 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.61: 64
        2.61 -     3.11: 3665
        3.11 -     3.60: 5373
        3.60 -     4.10: 6676
        4.10 -     4.60: 10272
  Nonbonded interactions: 26050
  Sorted by model distance:
  nonbonded pdb=" O   ILE A2396 "
            pdb=" OG  SER A2399 "
     model   vdw
     2.109 2.800
  nonbonded pdb=" O   TRP A2142 "
            pdb="HD21 ASN A2146 "
     model   vdw
     2.212 2.450
  nonbonded pdb=" O   ARG A2241 "
            pdb=" OG1 THR A2244 "
     model   vdw
     2.233 2.800
  nonbonded pdb=" O   MET A2467 "
            pdb=" ND1 HIS A2471 "
     model   vdw
     2.255 2.950
  nonbonded pdb=" O   GLY A2071 "
            pdb=" OG  SER A2074 "
     model   vdw
     2.273 2.800
  ... (remaining 26045 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.10 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:             8.930
  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:             0.130
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     24.170
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   36.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4393
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      :  0.002   0.030   4541  Z= 0.154
  Angle     :  0.619   7.070   6089  Z= 0.364
  Chirality :  0.039   0.162    620
  Planarity :  0.005   0.069    776
  Dihedral  : 13.157  75.227   1767
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 26.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.20 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.33), residues: 524
  helix:  0.10 (0.29), residues: 267
  sheet:  None (None), residues: 0
  loop : -1.28 (0.36), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A2234 
 HIS   0.004   0.001   HIS A2200 
 PHE   0.037   0.002   PHE A2078 
 TYR   0.018   0.001   TYR A2424 
 ARG   0.007   0.000   ARG A2506 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8396 (pp) cc_final: 0.7924 (pp)
REVERT: A 2154 MET cc_start: 0.1921 (mtt) cc_final: -0.0988 (mmm)
REVERT: A 2422 MET cc_start: 0.7409 (pmm) cc_final: 0.7105 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2889
  time to fit residues: 19.1658
Evaluate side-chains
  41 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2503 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4900 r_free = 0.4900 target = 0.224218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.203918 restraints weight = 41834.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.207767 restraints weight = 34661.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.209685 restraints weight = 25912.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4742 r_free = 0.4742    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4741 r_free = 0.4741    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4502
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   4541  Z= 0.138
  Angle     :  0.462   5.486   6089  Z= 0.261
  Chirality :  0.036   0.122    620
  Planarity :  0.004   0.061    776
  Dihedral  :  3.798  15.277    579
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 37.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.61 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.37), residues: 524
  helix:  0.96 (0.31), residues: 283
  sheet:  None (None), residues: 0
  loop : -1.00 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A2234 
 HIS   0.001   0.000   HIS A2200 
 PHE   0.017   0.002   PHE A2078 
 TYR   0.011   0.001   TYR A2249 
 ARG   0.005   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8043 (pp) cc_final: 0.7448 (pp)
REVERT: A 2154 MET cc_start: 0.1834 (mtt) cc_final: -0.1031 (mmm)
REVERT: A 2422 MET cc_start: 0.7621 (pmm) cc_final: 0.7039 (pmm)
REVERT: A 2434 LYS cc_start: 0.7430 (mmtp) cc_final: 0.6881 (mmtt)
REVERT: A 2465 TRP cc_start: 0.5655 (t60) cc_final: 0.4295 (t60)
REVERT: A 2574 PHE cc_start: 0.6243 (t80) cc_final: 0.5824 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.2277
  time to fit residues: 15.3116
Evaluate side-chains
  46 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0270
   chunk 41 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0980
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.4840

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.223374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.201686 restraints weight = 55047.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.207707 restraints weight = 40296.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.209505 restraints weight = 26858.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.4728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4729 r_free = 0.4729    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4729 r_free = 0.4729    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4484
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4541  Z= 0.099
  Angle     :  0.427   6.398   6089  Z= 0.237
  Chirality :  0.035   0.108    620
  Planarity :  0.004   0.056    776
  Dihedral  :  3.620  15.227    579
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 38.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.42 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.38), residues: 524
  helix:  1.37 (0.31), residues: 292
  sheet:  None (None), residues: 0
  loop : -0.75 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A2234 
 HIS   0.002   0.001   HIS A2200 
 PHE   0.021   0.001   PHE A2078 
 TYR   0.008   0.001   TYR A2103 
 ARG   0.007   0.000   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8035 (pp) cc_final: 0.7579 (pp)
REVERT: A 2465 TRP cc_start: 0.5693 (t60) cc_final: 0.4627 (t60)
REVERT: A 2472 ILE cc_start: 0.8073 (tp) cc_final: 0.7761 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2139
  time to fit residues: 15.0658
Evaluate side-chains
  48 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 38 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4865 r_free = 0.4865 target = 0.220225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.197293 restraints weight = 61659.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.203662 restraints weight = 44611.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.205378 restraints weight = 29523.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4695 r_free = 0.4695    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4695 r_free = 0.4695    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4615
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   4541  Z= 0.114
  Angle     :  0.431   5.446   6089  Z= 0.240
  Chirality :  0.036   0.110    620
  Planarity :  0.004   0.051    776
  Dihedral  :  3.668  15.823    579
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 43.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.01 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.39), residues: 524
  helix:  1.54 (0.31), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.66 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.001   0.000   HIS A2200 
 PHE   0.016   0.002   PHE A2078 
 TYR   0.006   0.001   TYR A2083 
 ARG   0.010   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8079 (pp) cc_final: 0.7567 (pp)
REVERT: A 2154 MET cc_start: 0.2404 (mpp) cc_final: 0.0673 (mtp)
REVERT: A 2465 TRP cc_start: 0.5606 (t60) cc_final: 0.4684 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2352
  time to fit residues: 16.5306
Evaluate side-chains
  51 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.210995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.191869 restraints weight = 51721.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.195829 restraints weight = 38782.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.198986 restraints weight = 28740.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4633 r_free = 0.4633    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4634 r_free = 0.4634    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4814
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4541  Z= 0.192
  Angle     :  0.611  10.168   6089  Z= 0.334
  Chirality :  0.040   0.154    620
  Planarity :  0.005   0.056    776
  Dihedral  :  4.504  21.746    579
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 58.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.22 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.37), residues: 524
  helix:  1.10 (0.31), residues: 279
  sheet:  None (None), residues: 0
  loop : -1.06 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A2511 
 HIS   0.004   0.001   HIS A2200 
 PHE   0.025   0.002   PHE A2064 
 TYR   0.012   0.002   TYR A2031 
 ARG   0.011   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8253 (pp) cc_final: 0.7663 (pp)
REVERT: A 2154 MET cc_start: 0.2830 (mpp) cc_final: 0.0915 (mtp)
REVERT: A 2465 TRP cc_start: 0.5725 (t60) cc_final: 0.4803 (t60)
REVERT: A 2472 ILE cc_start: 0.8507 (tp) cc_final: 0.8080 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2241
  time to fit residues: 15.9313
Evaluate side-chains
  46 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 25 optimal weight:    0.3980
   chunk 51 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   chunk 46 optimal weight:    0.0870
   chunk 23 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 9 optimal weight:    7.9990
   chunk 47 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.214866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.191494 restraints weight = 59380.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.198916 restraints weight = 43636.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.200188 restraints weight = 28934.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4633 r_free = 0.4633    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4633 r_free = 0.4633    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4750
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.033   4541  Z= 0.101
  Angle     :  0.430   4.860   6089  Z= 0.239
  Chirality :  0.036   0.109    620
  Planarity :  0.004   0.048    776
  Dihedral  :  3.929  18.117    579
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 46.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.41 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.38), residues: 524
  helix:  1.34 (0.30), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.77 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A2234 
 HIS   0.001   0.000   HIS A2086 
 PHE   0.027   0.001   PHE A2078 
 TYR   0.006   0.001   TYR A2031 
 ARG   0.007   0.001   ARG A2248 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8042 (pp) cc_final: 0.7529 (pp)
REVERT: A 2154 MET cc_start: 0.2499 (mpp) cc_final: 0.1006 (mtp)
REVERT: A 2432 ILE cc_start: 0.7353 (mt) cc_final: 0.7099 (mt)
REVERT: A 2461 ARG cc_start: 0.6500 (ttt180) cc_final: 0.5572 (mtp180)
REVERT: A 2465 TRP cc_start: 0.5583 (t60) cc_final: 0.4990 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2298
  time to fit residues: 16.3119
Evaluate side-chains
  49 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0070
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.3802

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.210099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.191747 restraints weight = 42766.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.196689 restraints weight = 34855.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.198679 restraints weight = 23585.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.4623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4623 r_free = 0.4623    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4623 r_free = 0.4623    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4820
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4541  Z= 0.146
  Angle     :  0.499   5.068   6089  Z= 0.277
  Chirality :  0.038   0.120    620
  Planarity :  0.004   0.048    776
  Dihedral  :  4.174  22.137    579
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 55.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.22 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.37), residues: 524
  helix:  1.28 (0.30), residues: 292
  sheet:  None (None), residues: 0
  loop : -0.92 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A2234 
 HIS   0.002   0.001   HIS A2200 
 PHE   0.022   0.002   PHE A2078 
 TYR   0.011   0.001   TYR A2082 
 ARG   0.009   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8224 (pp) cc_final: 0.7611 (pp)
REVERT: A 2154 MET cc_start: 0.2629 (mpp) cc_final: 0.0764 (mtp)
REVERT: A 2465 TRP cc_start: 0.5408 (t60) cc_final: 0.4659 (t60)
REVERT: A 2472 ILE cc_start: 0.8638 (tp) cc_final: 0.8226 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2223
  time to fit residues: 15.6115
Evaluate side-chains
  45 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0170
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0870
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2232 GLN
A2503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.212242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.190701 restraints weight = 60138.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.196583 restraints weight = 44647.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.198730 restraints weight = 30590.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4624 r_free = 0.4624    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4623 r_free = 0.4623    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4793
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4541  Z= 0.108
  Angle     :  0.454   5.846   6089  Z= 0.252
  Chirality :  0.037   0.179    620
  Planarity :  0.004   0.048    776
  Dihedral  :  4.040  20.834    579
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 50.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.81 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.38), residues: 524
  helix:  1.41 (0.30), residues: 292
  sheet:  None (None), residues: 0
  loop : -0.75 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A2511 
 HIS   0.001   0.000   HIS A2338 
 PHE   0.026   0.002   PHE A2078 
 TYR   0.021   0.001   TYR A2470 
 ARG   0.009   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8141 (pp) cc_final: 0.7586 (pp)
REVERT: A 2154 MET cc_start: 0.2552 (mpp) cc_final: 0.1103 (mtp)
REVERT: A 2472 ILE cc_start: 0.8405 (tp) cc_final: 0.7909 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2211
  time to fit residues: 15.5988
Evaluate side-chains
  48 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A2146 ASN
A2232 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.204562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.182644 restraints weight = 73447.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.188921 restraints weight = 53766.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.190882 restraints weight = 34638.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4528 r_free = 0.4528    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4528 r_free = 0.4528    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5052
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4541  Z= 0.225
  Angle     :  0.637   7.177   6089  Z= 0.353
  Chirality :  0.041   0.188    620
  Planarity :  0.005   0.047    776
  Dihedral  :  4.930  27.788    579
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 63.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.20 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.37), residues: 524
  helix:  0.82 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A2473 
 HIS   0.003   0.001   HIS A2338 
 PHE   0.030   0.003   PHE A2574 
 TYR   0.016   0.002   TYR A2083 
 ARG   0.018   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8278 (pp) cc_final: 0.7604 (pp)
REVERT: A 2154 MET cc_start: 0.2690 (mpp) cc_final: 0.0930 (mtp)
REVERT: A 2422 MET cc_start: 0.8213 (pmm) cc_final: 0.7507 (pmm)
REVERT: A 2424 TYR cc_start: 0.8041 (m-10) cc_final: 0.7714 (m-80)
REVERT: A 2472 ILE cc_start: 0.8576 (tp) cc_final: 0.8208 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1775
  time to fit residues: 13.8472
Evaluate side-chains
  51 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0170
   chunk 51 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.208483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.188873 restraints weight = 50668.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.194103 restraints weight = 35538.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.196927 restraints weight = 23616.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4610 r_free = 0.4610    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4610 r_free = 0.4610    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4908
moved from start:          0.5058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4541  Z= 0.120
  Angle     :  0.496   5.676   6089  Z= 0.276
  Chirality :  0.038   0.175    620
  Planarity :  0.004   0.046    776
  Dihedral  :  4.408  22.550    579
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 52.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.20 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.38), residues: 524
  helix:  1.17 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.86 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A2511 
 HIS   0.002   0.001   HIS A2547 
 PHE   0.027   0.002   PHE A2078 
 TYR   0.015   0.001   TYR A2470 
 ARG   0.012   0.001   ARG A2127 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8215 (pp) cc_final: 0.7676 (pp)
REVERT: A 2154 MET cc_start: 0.2545 (mpp) cc_final: 0.1223 (mtp)
REVERT: A 2424 TYR cc_start: 0.8274 (m-10) cc_final: 0.7921 (m-80)
REVERT: A 2472 ILE cc_start: 0.8466 (tp) cc_final: 0.8011 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1876
  time to fit residues: 14.0882
Evaluate side-chains
  48 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0670
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0570
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.210388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.189488 restraints weight = 60575.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.195646 restraints weight = 42265.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.197441 restraints weight = 27826.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4601 r_free = 0.4601    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4601 r_free = 0.4601    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4894
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4541  Z= 0.107
  Angle     :  0.453   5.640   6089  Z= 0.251
  Chirality :  0.037   0.173    620
  Planarity :  0.004   0.047    776
  Dihedral  :  3.984  19.085    579
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 49.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.41 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.38), residues: 524
  helix:  1.52 (0.31), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.68 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A2511 
 HIS   0.002   0.001   HIS A2338 
 PHE   0.025   0.002   PHE A2078 
 TYR   0.012   0.001   TYR A2470 
 ARG   0.011   0.001   ARG A2127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1899.16 seconds
wall clock time: 34 minutes 26.24 seconds (2066.24 seconds total)