Starting phenix.real_space_refine
on Wed Mar  5 14:56:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gg6_51325/03_2025/9gg6_51325_neut.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1329      2.51       5
     N     396      2.21       5
     O     411      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2142
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 714
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 2.52, per 1000 atoms: 1.18
  Number of scatterers: 2142
  At special positions: 0
  Unit cell: (117.008, 66.744, 35.432, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     411      8.00
     N     396      7.00
     C    1329      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: 0.47
  Conformation dependent library (CDL) restraints added in 269.4 milliseconds
  

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  498

  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: 0.57
  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: 0.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 717
        1.34 -     1.46: 294
        1.46 -     1.57: 1152
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 2169
  Sorted by residual:
  bond pdb=" C   GLY C 273 "
       pdb=" O   GLY C 273 "
    ideal  model  delta    sigma   weight residual
    1.243  1.234  0.009 9.30e-03 1.16e+04 9.51e-01
  bond pdb=" C   GLY A 273 "
       pdb=" O   GLY A 273 "
    ideal  model  delta    sigma   weight residual
    1.243  1.234  0.009 9.30e-03 1.16e+04 9.37e-01
  bond pdb=" C   GLY B 273 "
       pdb=" O   GLY B 273 "
    ideal  model  delta    sigma   weight residual
    1.243  1.235  0.008 9.30e-03 1.16e+04 7.36e-01
  bond pdb=" CA  LYS C 294 "
       pdb=" C   LYS C 294 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.009 1.34e-02 5.57e+03 4.17e-01
  bond pdb=" CA  LYS B 294 "
       pdb=" C   LYS B 294 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.008 1.34e-02 5.57e+03 3.95e-01
  ... (remaining 2164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 2860
        2.18 -     4.37: 38
        4.37 -     6.55: 3
        6.55 -     8.73: 0
        8.73 -    10.92: 3
  Bond angle restraints: 2904
  Sorted by residual:
  angle pdb=" CA  LEU C 315 "
        pdb=" CB  LEU C 315 "
        pdb=" CG  LEU C 315 "
      ideal   model   delta    sigma   weight residual
     116.30  127.22  -10.92 3.50e+00 8.16e-02 9.73e+00
  angle pdb=" CA  LEU B 315 "
        pdb=" CB  LEU B 315 "
        pdb=" CG  LEU B 315 "
      ideal   model   delta    sigma   weight residual
     116.30  127.17  -10.87 3.50e+00 8.16e-02 9.64e+00
  angle pdb=" CA  LEU A 315 "
        pdb=" CB  LEU A 315 "
        pdb=" CG  LEU A 315 "
      ideal   model   delta    sigma   weight residual
     116.30  127.16  -10.86 3.50e+00 8.16e-02 9.63e+00
  angle pdb=" C   LYS C 294 "
        pdb=" N   ASP C 295 "
        pdb=" CA  ASP C 295 "
      ideal   model   delta    sigma   weight residual
     120.90  124.21   -3.31 1.41e+00 5.03e-01 5.52e+00
  angle pdb=" C   LYS A 294 "
        pdb=" N   ASP A 295 "
        pdb=" CA  ASP A 295 "
      ideal   model   delta    sigma   weight residual
     120.90  124.21   -3.31 1.41e+00 5.03e-01 5.50e+00
  ... (remaining 2899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 1183
       17.73 -    35.47: 110
       35.47 -    53.20: 36
       53.20 -    70.94: 3
       70.94 -    88.67: 3
  Dihedral angle restraints: 1335
    sinusoidal: 549
      harmonic: 786
  Sorted by residual:
  dihedral pdb=" CB  LYS A 331 "
           pdb=" CG  LYS A 331 "
           pdb=" CD  LYS A 331 "
           pdb=" CE  LYS A 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.11   55.89     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CB  LYS C 331 "
           pdb=" CG  LYS C 331 "
           pdb=" CD  LYS C 331 "
           pdb=" CE  LYS C 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.14   55.86     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CB  LYS B 331 "
           pdb=" CG  LYS B 331 "
           pdb=" CD  LYS B 331 "
           pdb=" CE  LYS B 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.19   55.81     3      1.50e+01 4.44e-03 9.37e+00
  ... (remaining 1332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 196
       0.030 -    0.059: 65
       0.059 -    0.089: 12
       0.089 -    0.118: 51
       0.118 -    0.148: 6
  Chirality restraints: 330
  Sorted by residual:
  chirality pdb=" CG  LEU A 315 "
            pdb=" CB  LEU A 315 "
            pdb=" CD1 LEU A 315 "
            pdb=" CD2 LEU A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CG  LEU B 315 "
            pdb=" CB  LEU B 315 "
            pdb=" CD1 LEU B 315 "
            pdb=" CD2 LEU B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CG  LEU C 315 "
            pdb=" CB  LEU C 315 "
            pdb=" CD1 LEU C 315 "
            pdb=" CD2 LEU C 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 327 not shown)

  Planarity restraints: 375
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 363 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 364 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 364 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 363 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO C 364 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 364 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 364 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO B 364 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "    0.018 5.00e-02 4.00e+02
  ... (remaining 372 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 790
        2.89 -     3.39: 1604
        3.39 -     3.89: 3569
        3.89 -     4.40: 3374
        4.40 -     4.90: 7229
  Nonbonded interactions: 16566
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 281 "
            pdb=" OD2 ASP C 348 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" OD2 ASP A 348 "
            pdb=" NZ  LYS B 281 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" N   ASP C 295 "
            pdb=" OD1 ASP C 295 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" N   ASP B 295 "
            pdb=" OD1 ASP B 295 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" N   ASP A 295 "
            pdb=" OD1 ASP A 295 "
     model   vdw
     2.405 3.120
  ... (remaining 16561 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.730
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   16.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2169  Z= 0.136
  Angle     :  0.710  10.918   2904  Z= 0.346
  Chirality :  0.051   0.148    330
  Planarity :  0.004   0.032    375
  Dihedral  : 15.584  88.671    837
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.51 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.41), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 329 
 PHE   0.008   0.003   PHE A 346 
 TYR   0.003   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  294 LYS cc_start: 0.8025 (mttt) cc_final: 0.7709 (tttt)
REVERT: A  317 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7716 (tttm)
REVERT: A  321 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6828 (mmmm)
REVERT: B  294 LYS cc_start: 0.8088 (mttt) cc_final: 0.7372 (pttm)
REVERT: B  317 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8238 (tttm)
REVERT: B  321 LYS cc_start: 0.7489 (mmtt) cc_final: 0.5954 (pttp)
REVERT: C  294 LYS cc_start: 0.7979 (mttt) cc_final: 0.7769 (tttt)
REVERT: C  321 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6658 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2757
  time to fit residues: 16.8681
Evaluate side-chains
  43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 GLN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.106774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.093011 restraints weight = 2932.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.17
r_work: 0.3338 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2169  Z= 0.259
  Angle     :  0.643   8.327   2904  Z= 0.316
  Chirality :  0.051   0.138    330
  Planarity :  0.005   0.042    375
  Dihedral  :  4.446  10.926    291
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 20.48 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.44), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 329 
 PHE   0.007   0.002   PHE A 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.001   ARG C 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  294 LYS cc_start: 0.8118 (mttt) cc_final: 0.7832 (tttt)
REVERT: B  294 LYS cc_start: 0.8111 (mttt) cc_final: 0.7420 (pttm)
REVERT: B  321 LYS cc_start: 0.7814 (mmtt) cc_final: 0.6199 (pttm)
REVERT: B  342 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8491 (mt-10)
REVERT: B  351 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7999 (pt0)
REVERT: C  294 LYS cc_start: 0.8041 (mttt) cc_final: 0.7821 (tttt)
  outliers start: 19
  outliers final: 16
  residues processed: 52
  average time/residue: 0.2374
  time to fit residues: 13.6279
Evaluate side-chains
  51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.109996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.096154 restraints weight = 3053.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.25
r_work: 0.3390 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2169  Z= 0.138
  Angle     :  0.535   6.981   2904  Z= 0.259
  Chirality :  0.050   0.123    330
  Planarity :  0.003   0.028    375
  Dihedral  :  4.092  11.898    291
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 22.89 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.45), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.000   0.000   ARG B 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  294 LYS cc_start: 0.8052 (mttt) cc_final: 0.7750 (tttt)
REVERT: B  294 LYS cc_start: 0.8007 (mttt) cc_final: 0.7297 (pttm)
REVERT: B  321 LYS cc_start: 0.7731 (mmtt) cc_final: 0.6102 (pttp)
REVERT: B  349 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8553 (ttm170)
REVERT: B  351 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8154 (pt0)
REVERT: C  294 LYS cc_start: 0.7956 (mttt) cc_final: 0.7720 (tttt)
REVERT: C  351 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7719 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 50
  average time/residue: 0.2576
  time to fit residues: 14.3643
Evaluate side-chains
  53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0870
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.110467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096465 restraints weight = 2991.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.27
r_work: 0.3397 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2169  Z= 0.137
  Angle     :  0.494   6.366   2904  Z= 0.246
  Chirality :  0.049   0.122    330
  Planarity :  0.003   0.026    375
  Dihedral  :  3.978  12.355    291
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 24.50 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.45), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.000   0.000   ARG C 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7725 (mttt)
REVERT: A  294 LYS cc_start: 0.8043 (mttt) cc_final: 0.7720 (tttt)
REVERT: A  340 LYS cc_start: 0.8573 (mptt) cc_final: 0.8372 (mmtm)
REVERT: B  294 LYS cc_start: 0.8058 (mttt) cc_final: 0.7385 (pttm)
REVERT: B  321 LYS cc_start: 0.7760 (mmtt) cc_final: 0.6136 (pttm)
REVERT: B  349 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8368 (ttm170)
REVERT: B  351 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8019 (pt0)
REVERT: C  351 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7706 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 53
  average time/residue: 0.2381
  time to fit residues: 13.9510
Evaluate side-chains
  55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 24 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095172 restraints weight = 3085.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.28
r_work: 0.3369 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2169  Z= 0.156
  Angle     :  0.542   6.614   2904  Z= 0.267
  Chirality :  0.050   0.122    330
  Planarity :  0.003   0.029    375
  Dihedral  :  4.050  13.918    291
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 23.69 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.45), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.005   0.002   TYR B 310 
 ARG   0.000   0.000   ARG C 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7715 (mttt)
REVERT: A  294 LYS cc_start: 0.8148 (mttt) cc_final: 0.7845 (tttt)
REVERT: A  321 LYS cc_start: 0.7499 (mptt) cc_final: 0.7273 (mptt)
REVERT: B  294 LYS cc_start: 0.8085 (mttt) cc_final: 0.7397 (pttm)
REVERT: B  321 LYS cc_start: 0.7898 (mmtt) cc_final: 0.6198 (pttm)
REVERT: B  351 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8120 (pt0)
REVERT: C  351 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7655 (pt0)
  outliers start: 19
  outliers final: 14
  residues processed: 53
  average time/residue: 0.2343
  time to fit residues: 13.7819
Evaluate side-chains
  55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0570
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.9302

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
A 307 GLN
B 299 HIS
B 307 GLN
C 307 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.095240 restraints weight = 3054.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.31
r_work: 0.3366 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2169  Z= 0.155
  Angle     :  0.572   7.665   2904  Z= 0.278
  Chirality :  0.050   0.122    330
  Planarity :  0.003   0.031    375
  Dihedral  :  4.197  17.924    291
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 24.10 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.005   0.001   TYR B 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7725 (mttt)
REVERT: A  294 LYS cc_start: 0.8083 (mttt) cc_final: 0.7755 (tttt)
REVERT: A  321 LYS cc_start: 0.7529 (mptt) cc_final: 0.7327 (mptt)
REVERT: B  294 LYS cc_start: 0.8104 (mttt) cc_final: 0.7412 (pttm)
REVERT: B  321 LYS cc_start: 0.7964 (mmtt) cc_final: 0.6250 (pttp)
REVERT: B  351 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8097 (pt0)
REVERT: C  351 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7642 (pt0)
  outliers start: 19
  outliers final: 16
  residues processed: 53
  average time/residue: 0.2241
  time to fit residues: 13.2883
Evaluate side-chains
  57 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 0 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   chunk 11 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.7580

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.109428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095314 restraints weight = 3110.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.33
r_work: 0.3376 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2169  Z= 0.144
  Angle     :  0.549   6.794   2904  Z= 0.267
  Chirality :  0.050   0.122    330
  Planarity :  0.003   0.030    375
  Dihedral  :  4.180  17.806    291
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 24.90 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (mttt)
REVERT: A  294 LYS cc_start: 0.8127 (mttt) cc_final: 0.7829 (tttt)
REVERT: B  294 LYS cc_start: 0.8112 (mttt) cc_final: 0.7387 (pttm)
REVERT: B  321 LYS cc_start: 0.7969 (mmtt) cc_final: 0.6252 (pttp)
REVERT: B  351 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8082 (pt0)
REVERT: C  351 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7646 (pt0)
  outliers start: 17
  outliers final: 13
  residues processed: 52
  average time/residue: 0.2103
  time to fit residues: 12.2745
Evaluate side-chains
  53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  322 CYS
Chi-restraints excluded: chain C residue  351 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0570
   overall best weight:    0.9316

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.112705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.098493 restraints weight = 3056.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.33
r_work: 0.3440 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2169  Z= 0.097
  Angle     :  0.504   6.674   2904  Z= 0.244
  Chirality :  0.050   0.121    330
  Planarity :  0.003   0.026    375
  Dihedral  :  4.014  17.318    291
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 24.90 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.003   0.001   TYR B 310 
 ARG   0.000   0.000   ARG A 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7721 (mttt)
REVERT: A  294 LYS cc_start: 0.8057 (mttt) cc_final: 0.7799 (tttt)
REVERT: B  294 LYS cc_start: 0.8047 (mttt) cc_final: 0.7289 (pttm)
REVERT: B  321 LYS cc_start: 0.7819 (mmtt) cc_final: 0.6243 (pttp)
  outliers start: 15
  outliers final: 13
  residues processed: 48
  average time/residue: 0.2361
  time to fit residues: 12.6460
Evaluate side-chains
  51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  322 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 18 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.9982

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.108712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.094700 restraints weight = 3158.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.31
r_work: 0.3365 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2169  Z= 0.159
  Angle     :  0.546   7.100   2904  Z= 0.265
  Chirality :  0.050   0.125    330
  Planarity :  0.003   0.030    375
  Dihedral  :  4.272  18.479    291
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 24.50 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.005   0.002   TYR B 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7761 (mttt)
REVERT: A  294 LYS cc_start: 0.8106 (mttt) cc_final: 0.7809 (tttt)
REVERT: B  294 LYS cc_start: 0.8168 (mttt) cc_final: 0.7461 (pttm)
REVERT: B  321 LYS cc_start: 0.8006 (mmtt) cc_final: 0.6312 (pttp)
  outliers start: 15
  outliers final: 12
  residues processed: 47
  average time/residue: 0.2176
  time to fit residues: 11.4674
Evaluate side-chains
  51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  322 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0470
   overall best weight:    1.8222

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.108896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094986 restraints weight = 3128.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.29
r_work: 0.3370 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2169  Z= 0.148
  Angle     :  0.545   7.851   2904  Z= 0.264
  Chirality :  0.050   0.123    330
  Planarity :  0.003   0.029    375
  Dihedral  :  4.317  18.509    291
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 24.90 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7756 (mttt)
REVERT: A  294 LYS cc_start: 0.8114 (mttt) cc_final: 0.7825 (tttt)
REVERT: B  294 LYS cc_start: 0.8150 (mttt) cc_final: 0.7400 (pttm)
REVERT: B  321 LYS cc_start: 0.7977 (mmtt) cc_final: 0.6265 (pttp)
  outliers start: 16
  outliers final: 14
  residues processed: 48
  average time/residue: 0.2036
  time to fit residues: 10.9782
Evaluate side-chains
  52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  290 LYS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  269 GLN
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  322 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0040
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.3798

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.110560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.096750 restraints weight = 3022.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.28
r_work: 0.3398 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2169  Z= 0.122
  Angle     :  0.541   7.771   2904  Z= 0.258
  Chirality :  0.050   0.122    330
  Planarity :  0.003   0.027    375
  Dihedral  :  4.222  18.189    291
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 24.50 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.46), residues: 282
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.000   0.000   ARG B 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1775.48 seconds
wall clock time: 31 minutes 24.62 seconds (1884.62 seconds total)