Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 15:44:55 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2022/7n95_24250.pdb"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.001 sd=   0.018
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 7299
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 363
          Classifications: {'peptide': 121}
          Incomplete info: {'n_c_alpha_c_only': 121}
          Link IDs: {'PTRANS': 9, 'TRANS': 110, 'PCIS': 1}
          Unresolved chain link angles: 130
          Unresolved non-hydrogen bonds: 629
          Unresolved non-hydrogen angles: 854
          Unresolved non-hydrogen dihedrals: 335
          Unresolved non-hydrogen chiralities: 141
          Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 262
    Chain: "A"
      Number of atoms: 6936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2312, 6936
          Classifications: {'peptide': 2312}
          Incomplete info: {'n_c_alpha_c_only': 2312}
          Link IDs: {'PTRANS': 48, 'TRANS': 2262, 'PCIS': 1}
          Chain breaks: 2
          Unresolved chain link angles: 2360
          Unresolved non-hydrogen bonds: 12070
          Unresolved non-hydrogen angles: 16430
          Unresolved non-hydrogen dihedrals: 6269
          Unresolved non-hydrogen chiralities: 2838
          Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 179, 'PHE:plan': 131, 'GLU:plan': 207, 'ARG:plan': 47}
          Unresolved non-hydrogen planarities: 5066
  Time building chain proxies: 5.74, per 1000 atoms: 0.79
  Number of scatterers: 7299
  At special positions: 0
  Unit cell: (132.581, 145.309, 255.617, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 2
    Type Number    sf(0)
     N    2433      7.00
     C    4866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 1.91
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  0

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.42
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.32 -     1.36: 2429
        1.36 -     1.41: 0
        1.41 -     1.45: 256
        1.45 -     1.50: 2177
        1.50 -     1.54: 2433
  Bond restraints: 7295
  Sorted by residual:
  bond pdb=" CA  THR A2204 "
       pdb=" C   THR A2204 "
    ideal  model  delta    sigma   weight residual
    1.523  1.545 -0.022 1.56e-02 4.11e+03 1.91e+00
  bond pdb=" N   ASP A2145 "
       pdb=" CA  ASP A2145 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.37e+00
  bond pdb=" C   ASP A 181 "
       pdb=" N   LYS A 182 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.014 1.31e-02 5.83e+03 1.07e+00
  bond pdb=" N   GLU A1369 "
       pdb=" CA  GLU A1369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.72e-01
  bond pdb=" N   GLU A 329 "
       pdb=" CA  GLU A 329 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.52e-01
  ... (remaining 7290 not shown)

  Histogram of bond angle deviations from ideal:
      105.08 -   109.87: 753
      109.87 -   114.67: 1679
      114.67 -   119.47: 2528
      119.47 -   124.26: 2275
      124.26 -   129.06: 56
  Bond angle restraints: 7291
  Sorted by residual:
  angle pdb=" N   ILE A1684 "
        pdb=" CA  ILE A1684 "
        pdb=" C   ILE A1684 "
      ideal   model   delta    sigma   weight residual
     113.20  108.21    4.99 9.60e-01 1.09e+00 2.71e+01
  angle pdb=" N   GLU A1947 "
        pdb=" CA  GLU A1947 "
        pdb=" C   GLU A1947 "
      ideal   model   delta    sigma   weight residual
     110.91  116.95   -6.04 1.17e+00 7.31e-01 2.67e+01
  angle pdb=" C   ILE A 403 "
        pdb=" N   GLU A 404 "
        pdb=" CA  GLU A 404 "
      ideal   model   delta    sigma   weight residual
     120.31  113.31    7.00 1.52e+00 4.33e-01 2.12e+01
  angle pdb=" N   ASP A2126 "
        pdb=" CA  ASP A2126 "
        pdb=" C   ASP A2126 "
      ideal   model   delta    sigma   weight residual
     114.62  109.75    4.87 1.14e+00 7.69e-01 1.82e+01
  angle pdb=" N   ILE A1809 "
        pdb=" CA  ILE A1809 "
        pdb=" C   ILE A1809 "
      ideal   model   delta    sigma   weight residual
     113.53  109.48    4.05 9.80e-01 1.04e+00 1.71e+01
  ... (remaining 7286 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.18: 1953
        6.18 -    12.35: 414
       12.35 -    18.53: 56
       18.53 -    24.70: 5
       24.70 -    30.88: 1
  Dihedral angle restraints: 2429
    sinusoidal: 0
      harmonic: 2429
  Sorted by residual:
  dihedral pdb=" CA  GLU A1947 "
           pdb=" C   GLU A1947 "
           pdb=" N   TRP A1948 "
           pdb=" CA  TRP A1948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.12   30.88     0      5.00e+00 4.00e-02 3.81e+01
  dihedral pdb=" CA  ILE A 813 "
           pdb=" C   ILE A 813 "
           pdb=" N   GLU A 814 "
           pdb=" CA  GLU A 814 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.10  -23.90     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  LEU A1404 "
           pdb=" C   LEU A1404 "
           pdb=" N   THR A1405 "
           pdb=" CA  THR A1405 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.36  -21.64     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 2426 not shown)

  Chirality restraints: 0

  Planarity restraints: 0

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 1925
        3.04 -     3.50: 2617
        3.50 -     3.97: 4896
        3.97 -     4.43: 5866
        4.43 -     4.90: 10075
  Nonbonded interactions: 25379
  Sorted by model distance:
  nonbonded pdb=" N   ILE A1684 "
            pdb=" N   ASP A1685 "
     model   vdw
     2.573 2.560
  nonbonded pdb=" N   ILE A1031 "
            pdb=" N   ILE A1032 "
     model   vdw
     2.599 2.560
  nonbonded pdb=" N   ILE A1590 "
            pdb=" N   LYS A1591 "
     model   vdw
     2.606 2.560
  nonbonded pdb=" N   GLY A1667 "
            pdb=" N   ASP A1668 "
     model   vdw
     2.661 2.560
  nonbonded pdb=" N   VAL A1352 "
            pdb=" N   ARG A1353 "
     model   vdw
     2.662 2.560
  ... (remaining 25374 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
Set scattering table
  Set to: electron
  Number of scattering types: 2
    Type Number    sf(0)   Gaussians
     C    4866      2.51       5
     N    2433      2.21       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          16.260
  Check model and map are aligned:         0.110
  Convert atoms to be neutral:             0.060
  Process input model:                     21.810
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Set scattering table:                    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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
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   0.022   7295  Z= 0.153
  Angle     :  0.742   7.522   7291  Z= 0.486
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.054  30.879   2429
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 0.10
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  7.09 %
    Favored  : 92.33 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -1.14 (0.17), residues: 2425
  helix:  0.47 (0.21), residues: 597
  sheet: -0.38 (0.30), residues: 308
  loop : -1.40 (0.16), residues: 1520

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.179 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0650
  time to fit residues: 7.6565
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.127 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.0011
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 205 optimal weight:    3.9990
   chunk 184 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 124 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 190 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 115 optimal weight:   50.0000
   chunk 141 optimal weight:    0.9980
   chunk 220 optimal weight:    8.9990
   overall best weight:    1.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7295  Z= 0.258
  Angle     :  0.684   8.109   7291  Z= 0.442
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.224  23.556   2429
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  8.16 %
    Favored  : 91.30 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -1.43 (0.17), residues: 2425
  helix: -0.09 (0.21), residues: 535
  sheet: -0.57 (0.27), residues: 364
  loop : -1.42 (0.16), residues: 1526

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.214 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0608
  time to fit residues: 7.1674
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.116 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5434
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0770
   chunk 183 optimal weight:    9.9990
   chunk 150 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 221 optimal weight:    0.0060
   chunk 238 optimal weight:    9.9990
   chunk 196 optimal weight:    4.9990
   chunk 219 optimal weight:    0.2980
   chunk 75 optimal weight:    5.9990
   chunk 177 optimal weight:    2.9990
   overall best weight:    0.4556

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.001   0.010   7295  Z= 0.072
  Angle     :  0.347   3.612   7291  Z= 0.216
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  3.065  16.590   2429
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.03 %
    Favored  : 94.52 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -0.77 (0.17), residues: 2425
  helix:  1.10 (0.22), residues: 545
  sheet: -0.53 (0.28), residues: 379
  loop : -1.16 (0.16), residues: 1501

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.035 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0569
  time to fit residues: 6.8141
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.017 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 218 optimal weight:    9.9990
   chunk 166 optimal weight:    9.9990
   chunk 114 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0060
   chunk 105 optimal weight:    3.9990
   chunk 148 optimal weight:   10.0000
   chunk 221 optimal weight:    8.9990
   chunk 234 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 210 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    3.2202

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.8158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.121   7295  Z= 0.430
  Angle     :  1.005   8.948   7291  Z= 0.652
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  6.987  29.841   2429
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 13.20 %
    Favored  : 86.43 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.55 (0.16), residues: 2425
  helix: -1.59 (0.21), residues: 487
  sheet: -0.64 (0.29), residues: 309
  loop : -2.05 (0.14), residues: 1629

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.130 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0601
  time to fit residues: 7.2433
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.174 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4073
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 195 optimal weight:    3.9990
   chunk 133 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 174 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 200 optimal weight:    4.9990
   chunk 162 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 119 optimal weight:    3.9990
   chunk 210 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    2.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.8622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.070   7295  Z= 0.282
  Angle     :  0.716   6.468   7291  Z= 0.460
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.388  22.445   2429
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.46 %
    Favored  : 88.33 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.73 (0.16), residues: 2425
  helix: -1.58 (0.21), residues: 486
  sheet: -1.03 (0.29), residues: 325
  loop : -2.18 (0.15), residues: 1614

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.634 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0587
  time to fit residues: 7.1452
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.129 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 211 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 137 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0020
   chunk 235 optimal weight:    8.9990
   chunk 195 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 123 optimal weight:    0.4980
   overall best weight:    1.2392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.9029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.052   7295  Z= 0.171
  Angle     :  0.521   4.901   7291  Z= 0.330
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  4.279  19.714   2429
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.04 %
    Favored  : 87.75 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.40 (0.16), residues: 2425
  helix: -1.01 (0.23), residues: 488
  sheet: -0.81 (0.31), residues: 300
  loop : -2.05 (0.15), residues: 1637

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.129 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0654
  time to fit residues: 7.7546
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.124 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5998
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 226 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 133 optimal weight:    8.9990
   chunk 171 optimal weight:    0.0980
   chunk 197 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 234 optimal weight:    9.9990
   chunk 146 optimal weight:   10.0000
   chunk 142 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 144 optimal weight:    0.0000
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.9956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7295  Z= 0.267
  Angle     :  0.696   5.165   7291  Z= 0.448
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.331  21.596   2429
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 14.23 %
    Favored  : 85.53 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.76 (0.16), residues: 2425
  helix: -1.44 (0.23), residues: 429
  sheet: -1.21 (0.32), residues: 268
  loop : -2.20 (0.14), residues: 1728

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.130 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0619
  time to fit residues: 7.3365
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.018 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4669
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 93 optimal weight:    0.0370
   chunk 139 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0020
   chunk 45 optimal weight:    0.8980
   chunk 148 optimal weight:    9.9990
   chunk 159 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 184 optimal weight:    3.9990
   chunk 213 optimal weight:    8.9990
   overall best weight:    0.7870

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.9792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7295  Z= 0.113
  Angle     :  0.416   3.605   7291  Z= 0.262
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  3.631  20.078   2429
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.53 %
    Favored  : 90.31 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.36 (0.17), residues: 2425
  helix: -0.77 (0.24), residues: 476
  sheet: -0.83 (0.34), residues: 254
  loop : -2.07 (0.15), residues: 1695

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.131 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0602
  time to fit residues: 7.2448
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.145 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5448
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 224 optimal weight:    6.9990
   chunk 204 optimal weight:    0.0570
   chunk 218 optimal weight:    9.9990
   chunk 131 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 171 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 197 optimal weight:    5.9990
   chunk 206 optimal weight:   10.0000
   chunk 217 optimal weight:   10.0000
   chunk 143 optimal weight:    4.9990
   overall best weight:    3.2104

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          1.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.119   7295  Z= 0.420
  Angle     :  0.930  12.162   7291  Z= 0.602
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  6.392  29.991   2429
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 18.39 %
    Favored  : 81.32 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -3.24 (0.16), residues: 2425
  helix: -1.95 (0.23), residues: 404
  sheet: -1.31 (0.35), residues: 222
  loop : -2.52 (0.14), residues: 1799

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.107 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0627
  time to fit residues: 7.4939
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.097 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4950
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 230 optimal weight:   20.0000
   chunk 140 optimal weight:    9.9990
   chunk 109 optimal weight:    4.9990
   chunk 160 optimal weight:    0.9980
   chunk 242 optimal weight:   10.0000
   chunk 222 optimal weight:    0.0050
   chunk 192 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 153 optimal weight:    0.7980
   overall best weight:    1.9598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          1.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.075   7295  Z= 0.260
  Angle     :  0.658   6.221   7291  Z= 0.422
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.104  27.723   2429
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 13.90 %
    Favored  : 85.94 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -3.09 (0.16), residues: 2425
  helix: -1.73 (0.24), residues: 427
  sheet: -1.26 (0.36), residues: 220
  loop : -2.43 (0.14), residues: 1778

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

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

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4850 Ramachandran restraints generated.
    2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.194 
Fit side-chains
TARDY: cannot create tardy model for: "MET B  57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0660
  time to fit residues: 7.8428
Evaluate side-chains
  47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.127 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6055
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 205 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0170
   chunk 177 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0070
   chunk 193 optimal weight:    5.9990
   chunk 80 optimal weight:    0.2980
   chunk 198 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 169 optimal weight:    5.9990
   overall best weight:    1.0640

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.088620 restraints weight = 20950.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.083973 restraints weight = 22172.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.083558 restraints weight = 24946.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          1.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7295  Z= 0.145
  Angle     :  0.472   5.617   7291  Z= 0.297
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  3.970  22.205   2429
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 14.43 %
    Favored  : 85.40 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    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: -2.80 (0.17), residues: 2425
  helix: -1.16 (0.25), residues: 438
  sheet: -1.10 (0.37), residues: 219
  loop : -2.33 (0.14), residues: 1768

===============================================================================
Job complete
usr+sys time: 1748.90 seconds
wall clock time: 31 minutes 43.35 seconds (1903.35 seconds total)