Starting phenix.real_space_refine
on Wed Feb 12 02:17:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n9q_24259/02_2025/7n9q_24259.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 2
    Type Number    sf(0)   Gaussians
     C    4630      2.51       5
     N    2315      2.21       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6945
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2315, 6945
          Classifications: {'peptide': 2315}
          Incomplete info: {'n_c_alpha_c_only': 2315}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 2264}
          Chain breaks: 2
          Unresolved chain link angles: 2364
          Unresolved non-hydrogen bonds: 12079
          Unresolved non-hydrogen angles: 16444
          Unresolved non-hydrogen dihedrals: 6273
          Unresolved non-hydrogen chiralities: 2840
          Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 180, 'PHE:plan': 132, 'GLU:plan': 205, 'ARG:plan': 48}
          Unresolved non-hydrogen planarities: 5074
  Time building chain proxies: 7.07, per 1000 atoms: 1.02
  Number of scatterers: 6945
  At special positions: 0
  Unit cell: (134.703, 146.37, 256.677, 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    2315      7.00
     C    4630      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 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: 3.29
  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: 2.07 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: 2312
        1.36 -     1.41: 0
        1.41 -     1.45: 123
        1.45 -     1.50: 2192
        1.50 -     1.54: 2315
  Bond restraints: 6942
  Sorted by residual:
  bond pdb=" CA  VAL A1094 "
       pdb=" C   VAL A1094 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 8.80e-03 1.29e+04 2.76e+00
  bond pdb=" N   ASP A 442 "
       pdb=" CA  ASP A 442 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.54e+00
  bond pdb=" CA  ASP A1500 "
       pdb=" C   ASP A1500 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.009 8.40e-03 1.42e+04 1.04e+00
  bond pdb=" N   ASN A1839 "
       pdb=" CA  ASN A1839 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.99e-01
  bond pdb=" N   SER A1242 "
       pdb=" CA  SER A1242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.78e-01
  ... (remaining 6937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 6754
        2.29 -     4.57: 152
        4.57 -     6.86: 28
        6.86 -     9.15: 2
        9.15 -    11.43: 3
  Bond angle restraints: 6939
  Sorted by residual:
  angle pdb=" C   ALA A 441 "
        pdb=" N   ASP A 442 "
        pdb=" CA  ASP A 442 "
      ideal   model   delta    sigma   weight residual
     121.54  132.97  -11.43 1.91e+00 2.74e-01 3.58e+01
  angle pdb=" C   PHE A2069 "
        pdb=" N   ASP A2070 "
        pdb=" CA  ASP A2070 "
      ideal   model   delta    sigma   weight residual
     121.54  131.75  -10.21 1.91e+00 2.74e-01 2.86e+01
  angle pdb=" C   GLN A 193 "
        pdb=" N   ARG A 194 "
        pdb=" CA  ARG A 194 "
      ideal   model   delta    sigma   weight residual
     121.58  112.24    9.34 1.95e+00 2.63e-01 2.29e+01
  angle pdb=" N   TYR A2223 "
        pdb=" CA  TYR A2223 "
        pdb=" C   TYR A2223 "
      ideal   model   delta    sigma   weight residual
     114.75  109.14    5.61 1.26e+00 6.30e-01 1.98e+01
  angle pdb=" C   LYS A  76 "
        pdb=" N   GLU A  77 "
        pdb=" CA  GLU A  77 "
      ideal   model   delta    sigma   weight residual
     120.31  114.02    6.29 1.52e+00 4.33e-01 1.71e+01
  ... (remaining 6934 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.68: 1687
        5.68 -    11.36: 505
       11.36 -    17.04: 98
       17.04 -    22.71: 19
       22.71 -    28.39: 3
  Dihedral angle restraints: 2312
    sinusoidal: 0
      harmonic: 2312
  Sorted by residual:
  dihedral pdb=" CA  TYR A2213 "
           pdb=" C   TYR A2213 "
           pdb=" N   ASP A2214 "
           pdb=" CA  ASP A2214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.61   28.39     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  THR A1234 "
           pdb=" C   THR A1234 "
           pdb=" N   GLY A1235 "
           pdb=" CA  GLY A1235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.19   25.81     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  GLU A1212 "
           pdb=" C   GLU A1212 "
           pdb=" N   LEU A1213 "
           pdb=" CA  LEU A1213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.35  -23.65     0      5.00e+00 4.00e-02 2.24e+01
  ... (remaining 2309 not shown)

  Chirality restraints: 0

  Planarity restraints: 0

  Histogram of nonbonded interaction distances:
        2.60 -     3.06: 1995
        3.06 -     3.52: 2446
        3.52 -     3.98: 4853
        3.98 -     4.44: 6241
        4.44 -     4.90: 9761
  Nonbonded interactions: 25296
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 442 "
            pdb=" N   ASN A 443 "
     model   vdw
     2.600 2.560
  nonbonded pdb=" N   ASP A1812 "
            pdb=" N   LEU A1813 "
     model   vdw
     2.603 2.560
  nonbonded pdb=" N   ILE A1809 "
            pdb=" N   GLY A1810 "
     model   vdw
     2.606 2.560
  nonbonded pdb=" N   ASP A2214 "
            pdb=" N   MET A2215 "
     model   vdw
     2.618 2.560
  nonbonded pdb=" N   GLY A1088 "
            pdb=" N   PHE A1089 "
     model   vdw
     2.627 2.560
  ... (remaining 25291 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             8.360
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.000
  Set scattering table:                    0.070
  Process input model:                     22.320
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
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   0.016   6942  Z= 0.171
  Angle     :  0.883  11.435   6939  Z= 0.561
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  5.650  28.393   2312
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  8.92 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.16), residues: 2309
  helix:  0.26 (0.21), residues: 569
  sheet: -0.42 (0.26), residues: 374
  loop : -1.90 (0.16), residues: 1366


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.050 
Fit side-chains
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: 44
  average time/residue: 0.0584
  time to fit residues: 6.3334
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 195 optimal weight:    6.9990
   chunk 175 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 118 optimal weight:    0.4980
   chunk 93 optimal weight:    0.0020
   chunk 181 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0570
   chunk 110 optimal weight:    5.9990
   chunk 134 optimal weight:    2.9990
   chunk 209 optimal weight:    3.9990
   overall best weight:    0.8708

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.127629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.070710 restraints weight = 15854.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.069080 restraints weight = 18718.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.069058 restraints weight = 21451.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6942  Z= 0.126
  Angle     :  0.520   5.275   6939  Z= 0.326
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  4.362  22.589   2312
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  :  7.49 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.17), residues: 2309
  helix:  1.51 (0.22), residues: 553
  sheet: -0.54 (0.25), residues: 410
  loop : -1.82 (0.16), residues: 1346


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.066 
Fit side-chains
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: 44
  average time/residue: 0.0651
  time to fit residues: 7.0881
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   chunk 206 optimal weight:    8.9990
   chunk 141 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 185 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 134 optimal weight:    5.9990
   chunk 218 optimal weight:    6.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.104450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.051389 restraints weight = 15020.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.051389 restraints weight = 17248.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.051389 restraints weight = 17248.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.9467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   6942  Z= 0.455
  Angle     :  1.267  12.509   6939  Z= 0.802
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  8.412  32.235   2312
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 22.80
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 13.56 %
    Favored  : 85.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.90 (0.16), residues: 2309
  helix: -1.68 (0.27), residues: 302
  sheet: -1.27 (0.29), residues: 306
  loop : -2.28 (0.13), residues: 1701


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.853 
Fit side-chains
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: 44
  average time/residue: 0.0588
  time to fit residues: 6.4952
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 171 optimal weight:   10.0000
   chunk 189 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 170 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 193 optimal weight:    3.9990
   chunk 209 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 104 optimal weight:    7.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   overall best weight:    4.2388

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.099019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.049718 restraints weight = 16615.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.049718 restraints weight = 19048.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.049718 restraints weight = 19048.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          1.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   6942  Z= 0.461
  Angle     :  1.387  28.973   6939  Z= 0.857
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  9.478  44.851   2312
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 35.26
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  : 19.36 %
    Favored  : 79.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -4.11 (0.15), residues: 2309
  helix: -3.23 (0.22), residues: 341
  sheet: -1.86 (0.32), residues: 244
  loop : -3.00 (0.13), residues: 1724


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.971 
Fit side-chains
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: 44
  average time/residue: 0.0568
  time to fit residues: 6.3592
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 203 optimal weight:   10.0000
   chunk 115 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 150 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0270
   chunk 223 optimal weight:    4.9990
   chunk 143 optimal weight:   10.0000
   chunk 199 optimal weight:    0.0170
   chunk 206 optimal weight:    4.9990
   overall best weight:    2.4082

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.100689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.051115 restraints weight = 15999.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.051102 restraints weight = 18665.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.051102 restraints weight = 18687.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          1.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6942  Z= 0.275
  Angle     :  0.920  22.857   6939  Z= 0.562
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  7.089  30.124   2312
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 23.75
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  : 18.19 %
    Favored  : 80.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: -3.89 (0.15), residues: 2309
  helix: -2.54 (0.25), residues: 332
  sheet: -1.78 (0.32), residues: 264
  loop : -2.98 (0.13), residues: 1713


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.958 
Fit side-chains
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: 44
  average time/residue: 0.0571
  time to fit residues: 6.3519
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 153 optimal weight:    0.0170
   chunk 174 optimal weight:    3.9990
   chunk 148 optimal weight:    4.9990
   chunk 229 optimal weight:   30.0000
   chunk 165 optimal weight:    0.0980
   chunk 222 optimal weight:    6.9990
   chunk 197 optimal weight:   10.0000
   chunk 133 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0370
   chunk 216 optimal weight:    5.9990
   chunk 119 optimal weight:    8.9990
   overall best weight:    1.8300

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.101449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.052636 restraints weight = 16500.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.052636 restraints weight = 18929.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.052636 restraints weight = 18929.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          1.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6942  Z= 0.218
  Angle     :  0.773  19.763   6939  Z= 0.474
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  6.326  26.100   2312
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  : 18.93 %
    Favored  : 80.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.16), residues: 2309
  helix: -2.46 (0.25), residues: 339
  sheet: -1.96 (0.31), residues: 287
  loop : -3.02 (0.14), residues: 1683


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.989 
Fit side-chains
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: 44
  average time/residue: 0.0565
  time to fit residues: 6.3152
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 174 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 199 optimal weight:   10.0000
   chunk 142 optimal weight:    8.9990
   chunk 184 optimal weight:    0.0040
   chunk 103 optimal weight:    7.9990
   chunk 145 optimal weight:    3.9990
   chunk 135 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 149 optimal weight:   10.0000
   chunk 136 optimal weight:    3.9990
   overall best weight:    2.8000

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.097366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.049425 restraints weight = 16547.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.049425 restraints weight = 19130.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.049425 restraints weight = 19130.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          1.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6942  Z= 0.322
  Angle     :  0.982  20.230   6939  Z= 0.614
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  7.408  32.850   2312
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 28.92
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  : 22.91 %
    Favored  : 76.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: -4.22 (0.15), residues: 2309
  helix: -2.88 (0.24), residues: 312
  sheet: -2.10 (0.32), residues: 269
  loop : -3.18 (0.13), residues: 1728


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.036 
Fit side-chains
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: 44
  average time/residue: 0.0606
  time to fit residues: 6.8028
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0040
   chunk 91 optimal weight:    0.2980
   chunk 155 optimal weight:    4.9990
   chunk 129 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 184 optimal weight:    0.0570
   chunk 157 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 116 optimal weight:    4.9990
   chunk 220 optimal weight:    5.9990
   overall best weight:    1.6714

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.099918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.051744 restraints weight = 16734.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 14)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.050966 restraints weight = 18973.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.050125 restraints weight = 21174.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          1.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6942  Z= 0.200
  Angle     :  0.721  18.235   6939  Z= 0.446
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  6.061  25.291   2312
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  : 18.02 %
    Favored  : 81.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.04 (0.16), residues: 2309
  helix: -2.50 (0.26), residues: 308
  sheet: -1.92 (0.32), residues: 272
  loop : -3.12 (0.13), residues: 1729


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.004 
Fit side-chains
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: 44
  average time/residue: 0.0555
  time to fit residues: 6.2423
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 227 optimal weight:    9.9990
   chunk 155 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0030
   chunk 144 optimal weight:    9.9990
   chunk 156 optimal weight:   20.0000
   chunk 140 optimal weight:    0.0980
   chunk 12 optimal weight:    8.9990
   overall best weight:    3.4196

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.094971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2495 r_free = 0.2495 target = 0.047511 restraints weight = 17366.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2495 r_free = 0.2495 target = 0.047511 restraints weight = 19812.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2495 r_free = 0.2495 target = 0.047511 restraints weight = 19812.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          1.5301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6942  Z= 0.375
  Angle     :  1.059  19.709   6939  Z= 0.669
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  7.722  34.246   2312
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 33.46
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 26.29 %
    Favored  : 72.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: -4.39 (0.15), residues: 2309
  helix: -2.95 (0.26), residues: 271
  sheet: -2.00 (0.34), residues: 247
  loop : -3.36 (0.13), residues: 1791


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.047 
Fit side-chains
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: 44
  average time/residue: 0.0683
  time to fit residues: 7.3045
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 218 optimal weight:   30.0000
   chunk 140 optimal weight:    0.0970
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    0.4980
   chunk 17 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 212 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 155 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    2.9184

-------------------------------------------------------------------------------
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 = 0.3355 r_free = 0.3355 target = 0.095468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2501 r_free = 0.2501 target = 0.048435 restraints weight = 18113.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2483 r_free = 0.2483 target = 0.047685 restraints weight = 20347.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2468 r_free = 0.2468 target = 0.047083 restraints weight = 22448.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.2410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          1.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6942  Z= 0.323
  Angle     :  0.948  19.177   6939  Z= 0.601
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  7.194  33.139   2312
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 29.77
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  : 22.78 %
    Favored  : 76.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -4.49 (0.15), residues: 2309
  helix: -3.22 (0.24), residues: 286
  sheet: -2.02 (0.37), residues: 223
  loop : -3.38 (0.13), residues: 1800


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

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

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4618 Ramachandran restraints generated.
    2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.950 
Fit side-chains
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: 44
  average time/residue: 0.0592
  time to fit residues: 6.5839
Evaluate side-chains
  44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 181 optimal weight:    4.9990
   chunk 157 optimal weight:    9.9990
   chunk 207 optimal weight:    1.9990
   chunk 229 optimal weight:   50.0000
   chunk 141 optimal weight:   10.0000
   chunk 129 optimal weight:    2.9990
   chunk 222 optimal weight:    2.9990
   chunk 136 optimal weight:   20.0000
   chunk 133 optimal weight:    6.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3310 r_free = 0.3310 target = 0.093650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.047693 restraints weight = 18079.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2460 r_free = 0.2460 target = 0.046835 restraints weight = 20814.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2460 r_free = 0.2460 target = 0.046824 restraints weight = 23407.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.2399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          1.6284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6942  Z= 0.393
  Angle     :  1.101  20.851   6939  Z= 0.697
  Chirality :  0.000   0.000      0
  Planarity :  0.000   0.000      0
  Dihedral  :  7.944  47.455   2312
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 35.68
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 28.50 %
    Favored  : 70.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -4.70 (0.15), residues: 2309
  helix: -3.29 (0.24), residues: 282
  sheet: -2.18 (0.39), residues: 195
  loop : -3.54 (0.12), residues: 1832

Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2570.57 seconds
wall clock time: 46 minutes 18.85 seconds (2778.85 seconds total)