Starting phenix.real_space_refine
on Sun Mar 10 19:41:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_22325.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_22325.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_22325.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_22325.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/03_2024/7jgf_22325.pdb"
  }
  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
    Residue "A PHE 2064": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 2088": "OD1" <-> "OD2"
    Residue "A PHE 2118": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2130": "OE1" <-> "OE2"
    Residue "A GLU 2132": "OE1" <-> "OE2"
    Residue "A TYR 2158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2188": "OE1" <-> "OE2"
    Residue "A GLU 2199": "OE1" <-> "OE2"
    Residue "A TYR 2203": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2227": "OE1" <-> "OE2"
    Residue "A TYR 2231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 2256": "OD1" <-> "OD2"
    Residue "A PHE 2374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 2395": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 2397": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 2424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 2426": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2459": "OE1" <-> "OE2"
    Residue "A ASP 2466": "OD1" <-> "OD2"
    Residue "A TYR 2470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 2481": "NH1" <-> "NH2"
    Residue "A GLU 2491": "OE1" <-> "OE2"
    Residue "A PHE 2495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 2497": "OD1" <-> "OD2"
    Residue "A PHE 2504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2510": "OE1" <-> "OE2"
    Residue "A GLU 2513": "OE1" <-> "OE2"
    Residue "A ASP 2524": "OD1" <-> "OD2"
    Residue "A GLU 2534": "OE1" <-> "OE2"
    Residue "A TYR 2555": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2564": "OE1" <-> "OE2"
    Residue "A ASP 2571": "OD1" <-> "OD2"
    Residue "A GLU 2573": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.65, per 1000 atoms: 1.49
  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  - 3.50
        Amino acid           : False - 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: 1.64
  Conformation dependent library (CDL) restraints added in 2.2 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: 0.31
  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: 0.88

  Time building geometry restraints manager: 1.79 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:
      100.08 -   106.91: 93
      106.91 -   113.74: 2455
      113.74 -   120.57: 1986
      120.57 -   127.40: 1556
      127.40 -   134.23: 53
  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 2.200
  nonbonded pdb=" O   TRP A2142 "
            pdb="HD21 ASN A2146 "
     model   vdw
     2.212 1.850
  nonbonded pdb=" O   ARG A2241 "
            pdb=" OG1 THR A2244 "
     model   vdw
     2.233 2.200
  nonbonded pdb=" O   MET A2467 "
            pdb=" ND1 HIS A2471 "
     model   vdw
     2.255 2.350
  nonbonded pdb=" O   GLY A2071 "
            pdb=" OG  SER A2074 "
     model   vdw
     2.273 2.200
  ... (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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.110
  Extract box with map and model:          3.670
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     20.980
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.690
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.486 
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: 0.2689
  time to fit residues: 17.3280
Evaluate side-chains
  41 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4518
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057   4541  Z= 0.144
  Angle     :  0.461   5.408   6089  Z= 0.263
  Chirality :  0.036   0.112    620
  Planarity :  0.004   0.061    776
  Dihedral  :  3.796  15.247    579
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 42.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  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:  0.18 (0.37), residues: 524
  helix:  1.04 (0.31), residues: 283
  sheet:  None (None), residues: 0
  loop : -0.99 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A2234 
 HIS   0.001   0.000   HIS A2420 
 PHE   0.015   0.001   PHE A2064 
 TYR   0.013   0.001   TYR A2249 
 ARG   0.006   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
  56 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8302 (pp) cc_final: 0.7730 (pp)
REVERT: A 2154 MET cc_start: 0.1860 (mtt) cc_final: -0.0862 (mmm)
REVERT: A 2198 GLN cc_start: 0.8732 (pp30) cc_final: 0.8510 (pp30)
REVERT: A 2434 LYS cc_start: 0.7348 (mmtp) cc_final: 0.6821 (mmtt)
REVERT: A 2461 ARG cc_start: 0.6836 (ttt180) cc_final: 0.6180 (ttm170)
REVERT: A 2465 TRP cc_start: 0.5332 (t60) cc_final: 0.3999 (t60)
REVERT: A 2574 PHE cc_start: 0.5505 (t80) cc_final: 0.5187 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2143
  time to fit residues: 14.7045
Evaluate side-chains
  47 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0870
   chunk 47 optimal weight:    0.0030
   chunk 16 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.4568

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

Flipped N/Q/H residues before XYZ refinement:
** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4511
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.027   4541  Z= 0.092
  Angle     :  0.409   4.872   6089  Z= 0.231
  Chirality :  0.035   0.107    620
  Planarity :  0.004   0.056    776
  Dihedral  :  3.640  15.139    579
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 40.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  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:  0.56 (0.38), residues: 524
  helix:  1.33 (0.32), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.79 (0.43), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A2234 
 HIS   0.003   0.000   HIS A2200 
 PHE   0.019   0.001   PHE A2078 
 TYR   0.007   0.001   TYR A2083 
 ARG   0.005   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 fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8328 (pp) cc_final: 0.7854 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2236
  time to fit residues: 15.6525
Evaluate side-chains
  46 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 36 optimal weight:    0.0370
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4500
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.042   4541  Z= 0.085
  Angle     :  0.394   4.605   6089  Z= 0.219
  Chirality :  0.035   0.107    620
  Planarity :  0.004   0.053    776
  Dihedral  :  3.497  14.680    579
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 42.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  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:  0.98 (0.39), residues: 524
  helix:  1.66 (0.31), residues: 292
  sheet:  None (None), residues: 0
  loop : -0.64 (0.45), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A2234 
 HIS   0.001   0.000   HIS A2200 
 PHE   0.016   0.001   PHE A2078 
 TYR   0.007   0.001   TYR A2249 
 ARG   0.009   0.000   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
  56 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.537 
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: 0.8311 (pp) cc_final: 0.7852 (pp)
REVERT: A 2154 MET cc_start: 0.1742 (mpp) cc_final: -0.0446 (mmm)
REVERT: A 2432 ILE cc_start: 0.6811 (mt) cc_final: 0.6583 (mt)
REVERT: A 2461 ARG cc_start: 0.6628 (ttt180) cc_final: 0.6392 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2161
  time to fit residues: 14.9810
Evaluate side-chains
  51 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4765
moved from start:          0.3309

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= 0.179
  Angle     :  0.568   8.671   6089  Z= 0.316
  Chirality :  0.039   0.140    620
  Planarity :  0.005   0.050    776
  Dihedral  :  4.229  19.618    579
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 58.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.03 %
    Favored  : 97.57 %
  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:  0.35 (0.37), residues: 524
  helix:  1.21 (0.31), residues: 281
  sheet:  None (None), residues: 0
  loop : -0.92 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A2234 
 HIS   0.004   0.001   HIS A2200 
 PHE   0.022   0.002   PHE A2078 
 TYR   0.014   0.001   TYR A2082 
 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
  55 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.474 
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: 0.8410 (pp) cc_final: 0.7844 (pp)
REVERT: A 2154 MET cc_start: 0.2242 (mpp) cc_final: 0.0563 (mtp)
REVERT: A 2415 ARG cc_start: 0.7306 (mmt180) cc_final: 0.6940 (mtm-85)
REVERT: A 2465 TRP cc_start: 0.5486 (t60) cc_final: 0.4725 (t60)
REVERT: A 2472 ILE cc_start: 0.8299 (tp) cc_final: 0.8050 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.2320
  time to fit residues: 15.6270
Evaluate side-chains
  49 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 51 optimal weight:    0.3980
   chunk 42 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:    0.2980
   chunk 49 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0050
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4657
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.028   4541  Z= 0.100
  Angle     :  0.435   6.322   6089  Z= 0.239
  Chirality :  0.036   0.115    620
  Planarity :  0.004   0.048    776
  Dihedral  :  3.836  17.187    579
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 49.51
  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:  0.69 (0.38), residues: 524
  helix:  1.45 (0.31), 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   0.026   0.001   PHE A2078 
 TYR   0.010   0.001   TYR A2031 
 ARG   0.005   0.001   ARG A2127 

*********************** 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
  57 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.395 
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: 0.8347 (pp) cc_final: 0.7851 (pp)
REVERT: A 2154 MET cc_start: 0.2035 (mpp) cc_final: 0.0428 (mtp)
REVERT: A 2415 ARG cc_start: 0.7165 (mmt180) cc_final: 0.6908 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2202
  time to fit residues: 15.3719
Evaluate side-chains
  48 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    0.0470
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0470
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4652
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.022   4541  Z= 0.094
  Angle     :  0.417   5.062   6089  Z= 0.232
  Chirality :  0.036   0.112    620
  Planarity :  0.004   0.049    776
  Dihedral  :  3.673  16.593    579
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 50.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  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:  0.79 (0.38), residues: 524
  helix:  1.51 (0.31), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.68 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A2465 
 HIS   0.001   0.000   HIS A2338 
 PHE   0.025   0.001   PHE A2078 
 TYR   0.020   0.001   TYR A2470 
 ARG   0.007   0.000   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
  56 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.521 
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: 0.8362 (pp) cc_final: 0.7876 (pp)
REVERT: A 2154 MET cc_start: 0.2191 (mpp) cc_final: 0.0551 (mtp)
REVERT: A 2198 GLN cc_start: 0.8666 (pp30) cc_final: 0.8464 (pp30)
REVERT: A 2415 ARG cc_start: 0.7171 (mmt180) cc_final: 0.6825 (mtm-85)
REVERT: A 2432 ILE cc_start: 0.7476 (mt) cc_final: 0.7265 (mt)
REVERT: A 2461 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6074 (ttm170)
REVERT: A 2472 ILE cc_start: 0.8472 (tp) cc_final: 0.8216 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2301
  time to fit residues: 15.8741
Evaluate side-chains
  46 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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**
A2232 GLN
A2503 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4713
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4541  Z= 0.115
  Angle     :  0.448   5.073   6089  Z= 0.250
  Chirality :  0.036   0.112    620
  Planarity :  0.004   0.048    776
  Dihedral  :  3.750  18.270    579
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 52.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  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:  0.84 (0.38), residues: 524
  helix:  1.60 (0.31), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.74 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A2234 
 HIS   0.002   0.000   HIS A2338 
 PHE   0.024   0.002   PHE A2078 
 TYR   0.012   0.001   TYR A2470 
 ARG   0.010   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
  58 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.514 
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: symmetry clash
REVERT: A 2093 LEU cc_start: 0.8372 (pp) cc_final: 0.7851 (pp)
REVERT: A 2154 MET cc_start: 0.2049 (mpp) cc_final: 0.0418 (mtp)
REVERT: A 2415 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6834 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2160
  time to fit residues: 15.4263
Evaluate side-chains
  48 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0870
   chunk 14 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 47 optimal weight:    8.9990
   chunk 31 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0000
   overall best weight:    0.4162

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4678
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.028   4541  Z= 0.094
  Angle     :  0.416   5.027   6089  Z= 0.231
  Chirality :  0.035   0.109    620
  Planarity :  0.004   0.047    776
  Dihedral  :  3.611  16.609    579
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 49.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  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:  1.07 (0.39), residues: 524
  helix:  1.68 (0.31), residues: 296
  sheet:  None (None), residues: 0
  loop : -0.57 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A2507 
 HIS   0.001   0.000   HIS A2338 
 PHE   0.024   0.001   PHE A2078 
 TYR   0.012   0.001   TYR A2470 
 ARG   0.009   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
  56 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.525 
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: 0.8317 (pp) cc_final: 0.7828 (pp)
REVERT: A 2154 MET cc_start: 0.2249 (mpp) cc_final: 0.1047 (mtp)
REVERT: A 2415 ARG cc_start: 0.7159 (mmt180) cc_final: 0.6840 (mtm-85)
REVERT: A 2472 ILE cc_start: 0.8292 (tp) cc_final: 0.7973 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2219
  time to fit residues: 15.2592
Evaluate side-chains
  48 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 48 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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**
A2232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4745
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4541  Z= 0.121
  Angle     :  0.464   8.148   6089  Z= 0.256
  Chirality :  0.037   0.122    620
  Planarity :  0.004   0.047    776
  Dihedral  :  3.745  18.082    579
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 55.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  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:  0.96 (0.39), residues: 524
  helix:  1.65 (0.31), residues: 292
  sheet:  None (None), residues: 0
  loop : -0.67 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A2234 
 HIS   0.002   0.000   HIS A2338 
 PHE   0.024   0.002   PHE A2078 
 TYR   0.010   0.001   TYR A2083 
 ARG   0.010   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
  56 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.538 
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: 0.8406 (pp) cc_final: 0.7891 (pp)
REVERT: A 2154 MET cc_start: 0.2410 (mpp) cc_final: 0.0797 (mtp)
REVERT: A 2472 ILE cc_start: 0.8408 (tp) cc_final: 0.8105 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2266
  time to fit residues: 15.5845
Evaluate side-chains
  43 residues out of total 487 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0040
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0000
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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
A2420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.217354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.201135 restraints weight = 39001.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.204811 restraints weight = 31769.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.205721 restraints weight = 24153.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4725 r_free = 0.4725    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4724 r_free = 0.4724    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4612
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.026   4541  Z= 0.096
  Angle     :  0.430   5.672   6089  Z= 0.238
  Chirality :  0.036   0.126    620
  Planarity :  0.004   0.047    776
  Dihedral  :  3.630  16.854    579
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 50.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  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:  1.11 (0.39), residues: 524
  helix:  1.78 (0.31), residues: 291
  sheet:  None (None), residues: 0
  loop : -0.60 (0.45), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A2234 
 HIS   0.002   0.000   HIS A2338 
 PHE   0.024   0.001   PHE A2078 
 TYR   0.011   0.001   TYR A2470 
 ARG   0.008   0.001   ARG A2127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1366.51 seconds
wall clock time: 25 minutes 22.95 seconds (1522.95 seconds total)