Starting phenix.real_space_refine
on Wed Mar  5 14:16:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eoe_19852/03_2025/9eoe_19852.cif"
  }
  resolution = 2.3
  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=   0.003
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       2      5.16       5
     C     372      2.51       5
     N     109      2.21       5
     O     112      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 595
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 595
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 77, 588
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
      Conformer: "B"
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
          bond proxies already assigned to first conformer: 588
  Time building chain proxies: 1.09, per 1000 atoms: 1.83
  Number of scatterers: 595
  At special positions: 0
  Unit cell: (87.344, 71.688, 21.424, 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       2     16.00
     O     112      8.00
     N     109      7.00
     C     372      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: 0.09
  Conformation dependent library (CDL) restraints added in 205.8 milliseconds
  

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  136

  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: 1.91
  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: 0.13 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 116
        1.32 -     1.44: 125
        1.44 -     1.56: 361
        1.56 -     1.68: 0
        1.68 -     1.80: 3
  Bond restraints: 605
  Sorted by residual:
  bond pdb=" C   GLN A 336 "
       pdb=" N  BVAL A 337 "
    ideal  model  delta    sigma   weight residual
    1.331  1.382 -0.052 1.43e-02 4.89e+03 1.30e+01
  bond pdb=" CA  SER A 341 "
       pdb=" CB  SER A 341 "
    ideal  model  delta    sigma   weight residual
    1.533  1.486  0.047 1.90e-02 2.77e+03 6.12e+00
  bond pdb=" C  BVAL A 337 "
       pdb=" N   GLU A 338 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.033 1.35e-02 5.49e+03 6.05e+00
  bond pdb=" CA  SER A 324 "
       pdb=" CB  SER A 324 "
    ideal  model  delta    sigma   weight residual
    1.528  1.490  0.038 1.66e-02 3.63e+03 5.29e+00
  bond pdb=" CB  HIS A 329 "
       pdb=" CG  HIS A 329 "
    ideal  model  delta    sigma   weight residual
    1.497  1.468  0.029 1.40e-02 5.10e+03 4.19e+00
  ... (remaining 600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 563
        1.35 -     2.70: 175
        2.70 -     4.05: 49
        4.05 -     5.40: 20
        5.40 -     6.75: 3
  Bond angle restraints: 810
  Sorted by residual:
  angle pdb=" C   ILE A 354 "
        pdb=" CA  ILE A 354 "
        pdb=" CB  ILE A 354 "
      ideal   model   delta    sigma   weight residual
     110.28  117.03   -6.75 1.58e+00 4.01e-01 1.83e+01
  angle pdb=" C   ARG A 349 "
        pdb=" CA  ARG A 349 "
        pdb=" CB  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     112.09  118.32   -6.23 1.54e+00 4.22e-01 1.64e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.87   -5.18 1.33e+00 5.65e-01 1.52e+01
  angle pdb=" CA  HIS A 329 "
        pdb=" CB  HIS A 329 "
        pdb=" CG  HIS A 329 "
      ideal   model   delta    sigma   weight residual
     113.80  110.39    3.41 1.00e+00 1.00e+00 1.17e+01
  angle pdb=" CA  GLY A 333 "
        pdb=" C   GLY A 333 "
        pdb=" O   GLY A 333 "
      ideal   model   delta    sigma   weight residual
     121.58  118.61    2.97 9.00e-01 1.23e+00 1.09e+01
  ... (remaining 805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    14.31: 323
       14.31 -    28.60: 37
       28.60 -    42.89: 4
       42.89 -    57.19: 2
       57.19 -    71.48: 4
  Dihedral angle restraints: 370
    sinusoidal: 155
      harmonic: 215
  Sorted by residual:
  dihedral pdb=" C   ARG A 349 "
           pdb=" N   ARG A 349 "
           pdb=" CA  ARG A 349 "
           pdb=" CB  ARG A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.21   13.61     0      2.50e+00 1.60e-01 2.97e+01
  dihedral pdb=" C   ILE A 354 "
           pdb=" N   ILE A 354 "
           pdb=" CA  ILE A 354 "
           pdb=" CB  ILE A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.59   11.59     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" N   ARG A 349 "
           pdb=" C   ARG A 349 "
           pdb=" CA  ARG A 349 "
           pdb=" CB  ARG A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.23  -10.43     0      2.50e+00 1.60e-01 1.74e+01
  ... (remaining 367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 69
       0.097 -    0.194: 16
       0.194 -    0.291: 3
       0.291 -    0.388: 1
       0.388 -    0.485: 1
  Chirality restraints: 90
  Sorted by residual:
  chirality pdb=" CA  ARG A 349 "
            pdb=" N   ARG A 349 "
            pdb=" C   ARG A 349 "
            pdb=" CB  ARG A 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.49 2.00e-01 2.50e+01 5.89e+00
  chirality pdb=" CA  ILE A 354 "
            pdb=" N   ILE A 354 "
            pdb=" C   ILE A 354 "
            pdb=" CB  ILE A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.14    0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CB  ILE A 354 "
            pdb=" CA  ILE A 354 "
            pdb=" CG1 ILE A 354 "
            pdb=" CG2 ILE A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 87 not shown)

  Planarity restraints: 104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 349 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.20e+00
        pdb=" C   ARG A 349 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ARG A 349 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL A 350 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 311 "   -0.011 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" C   LYS A 311 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LYS A 311 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 312 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 336 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.85e+00
        pdb=" C   GLN A 336 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLN A 336 "   -0.013 2.00e-02 2.50e+03
        pdb=" N  BVAL A 337 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 101 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.08: 324
        3.08 -     3.53: 488
        3.53 -     3.99: 652
        3.99 -     4.44: 563
        4.44 -     4.90: 980
  Nonbonded interactions: 3007
  Sorted by model distance:
  nonbonded pdb=" N   SER A 356 "
            pdb=" O   SER A 356 "
     model   vdw
     2.621 2.496
  nonbonded pdb=" O   LEU A 325 "
            pdb=" CA  GLY A 326 "
     model   vdw
     2.672 2.752
  nonbonded pdb=" O   LYS A 331 "
            pdb=" CB  LYS A 331 "
     model   vdw
     2.690 2.752
  nonbonded pdb=" N   ASN A 368 "
            pdb=" O   ASN A 368 "
     model   vdw
     2.697 2.496
  nonbonded pdb=" N   CYS A 322 "
            pdb=" O   CYS A 322 "
     model   vdw
     2.699 2.496
  ... (remaining 3002 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 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:             3.280
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     8.650
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.010
  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:12.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
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      :  0.009   0.052    605  Z= 0.611
  Angle     :  1.545   6.752    810  Z= 0.993
  Chirality :  0.104   0.485     90
  Planarity :  0.008   0.037    104
  Dihedral  : 14.876  71.479    234
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  :  4.41 %
    Favored  : 91.18 %
  Cbeta Deviations :  2.94 %
  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: -3.08 (0.69), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.52), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.005   HIS A 330 
 PHE   0.010   0.003   PHE A 346 
 TYR   0.012   0.004   TYR A 310 
 ARG   0.004   0.001   ARG A 349 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.7490 (tmtt) cc_final: 0.6954 (ttmt)
REVERT: A  331 LYS cc_start: 0.7934 (mttt) cc_final: 0.7670 (mttt)
REVERT: A  347 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7843 (pttt)
REVERT: A  351 GLN cc_start: 0.7535 (tt0) cc_final: 0.7258 (tt0)
REVERT: A  353 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7968 (mtpt)
REVERT: A  357 LEU cc_start: 0.7823 (pp) cc_final: 0.7431 (tp)
REVERT: A  369 LYS cc_start: 0.7898 (ptmt) cc_final: 0.6643 (tppt)
REVERT: A  375 LYS cc_start: 0.7716 (tttt) cc_final: 0.7354 (tttm)
  outliers start: 3
  outliers final: 2
  residues processed: 23
  average time/residue: 1.3617
  time to fit residues: 31.5557
Evaluate side-chains
  21 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    4.6657

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.205515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.183182 restraints weight = 3512.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 6.11
r_work: 0.3897 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3891 r_free = 0.3891    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060    605  Z= 0.248
  Angle     :  0.938   8.407    810  Z= 0.469
  Chirality :  0.058   0.173     90
  Planarity :  0.006   0.046    104
  Dihedral  : 10.328  49.906     85
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 17.65 %
    Favored  : 76.47 %
  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: -3.02 (0.66), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.50), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 329 
 PHE   0.005   0.002   PHE A 378 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.003   0.001   ARG A 349 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6354 (ptm-80)
REVERT: A  369 LYS cc_start: 0.7751 (ptmt) cc_final: 0.6666 (tppt)
  outliers start: 4
  outliers final: 1
  residues processed: 21
  average time/residue: 1.5528
  time to fit residues: 32.8261
Evaluate side-chains
  15 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    2.6657

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.206046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.194897 restraints weight = 564.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 0.61
r_work: 0.4085 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4007 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4006 r_free = 0.4006    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3999 r_free = 0.3999    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047    605  Z= 0.167
  Angle     :  0.740   6.915    810  Z= 0.373
  Chirality :  0.053   0.138     90
  Planarity :  0.005   0.047    104
  Dihedral  :  9.029  45.754     83
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 23.53 %
    Favored  : 73.53 %
  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: -2.83 (0.66), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.50), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 329 
 PHE   0.003   0.001   PHE A 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.002   0.001   ARG A 349 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6251 (ptm-80)
REVERT: A  369 LYS cc_start: 0.7668 (ptmt) cc_final: 0.6614 (tppt)
  outliers start: 2
  outliers final: 1
  residues processed: 15
  average time/residue: 1.2728
  time to fit residues: 19.2813
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.9987

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.206641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.183897 restraints weight = 1789.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 4.64
r_work: 0.3931 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039    605  Z= 0.141
  Angle     :  0.708   6.074    810  Z= 0.344
  Chirality :  0.052   0.130     90
  Planarity :  0.005   0.047    104
  Dihedral  :  7.538  39.681     83
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.12 %
    Favored  : 76.47 %
  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: -2.47 (0.70), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.53), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.002   0.001   ARG A 349 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6891 (ptp90)
REVERT: A  369 LYS cc_start: 0.7734 (ptmt) cc_final: 0.6585 (tppt)
  outliers start: 2
  outliers final: 1
  residues processed: 15
  average time/residue: 1.2722
  time to fit residues: 19.2718
Evaluate side-chains
  17 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    3.9320

-------------------------------------------------------------------------------
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 = 0.4369 r_free = 0.4369 target = 0.204213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.181045 restraints weight = 3283.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 4.84
r_work: 0.3903 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3899 r_free = 0.3899    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3899 r_free = 0.3899    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052    605  Z= 0.204
  Angle     :  0.808   6.540    810  Z= 0.400
  Chirality :  0.056   0.150     90
  Planarity :  0.006   0.052    104
  Dihedral  :  9.347  49.614     83
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.65 %
    Favored  : 77.94 %
  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: -2.49 (0.70), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.53), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 PHE   0.005   0.002   PHE A 346 
 TYR   0.009   0.003   TYR A 310 
 ARG   0.003   0.002   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6413 (ptm-80)
REVERT: A  369 LYS cc_start: 0.7861 (ptmt) cc_final: 0.6767 (tppt)
  outliers start: 2
  outliers final: 1
  residues processed: 15
  average time/residue: 1.3184
  time to fit residues: 19.9631
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.0650

-------------------------------------------------------------------------------
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 = 0.4427 r_free = 0.4427 target = 0.209693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.187209 restraints weight = 2487.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 4.74
r_work: 0.3973 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029    605  Z= 0.110
  Angle     :  0.652   6.549    810  Z= 0.306
  Chirality :  0.050   0.123     90
  Planarity :  0.005   0.046    104
  Dihedral  :  6.187  28.684     83
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 17.65 %
    Favored  : 76.47 %
  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: -2.26 (0.74), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.56), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 329 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.7506 (pttm) cc_final: 0.7230 (ptmm)
REVERT: A  369 LYS cc_start: 0.7699 (ptmt) cc_final: 0.6603 (tppt)
  outliers start: 3
  outliers final: 1
  residues processed: 20
  average time/residue: 1.4749
  time to fit residues: 29.7099
Evaluate side-chains
  20 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.6653

-------------------------------------------------------------------------------
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 = 0.4405 r_free = 0.4405 target = 0.207791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.185478 restraints weight = 1896.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 4.57
r_work: 0.3945 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034    605  Z= 0.125
  Angle     :  0.677   6.662    810  Z= 0.320
  Chirality :  0.051   0.125     90
  Planarity :  0.005   0.046    104
  Dihedral  :  6.083  28.923     83
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.12 %
    Favored  : 77.94 %
  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 (0.76), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.58), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.001   0.001   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.7526 (pttm) cc_final: 0.7235 (ptmm)
REVERT: A  369 LYS cc_start: 0.7760 (ptmt) cc_final: 0.6649 (tppt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 1.4704
  time to fit residues: 29.6176
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 2 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    2.1320

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.207329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.184692 restraints weight = 1973.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 5.18
r_work: 0.3924 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037    605  Z= 0.140
  Angle     :  0.706   6.870    810  Z= 0.336
  Chirality :  0.052   0.128     90
  Planarity :  0.005   0.046    104
  Dihedral  :  6.358  31.415     83
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.12 %
    Favored  : 77.94 %
  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 (0.76), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.58), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.002   0.001   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.7807 (ptmt) cc_final: 0.6675 (tppt)
  outliers start: 1
  outliers final: 1
  residues processed: 15
  average time/residue: 1.3355
  time to fit residues: 20.2270
Evaluate side-chains
  16 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.9317

-------------------------------------------------------------------------------
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 = 0.4433 r_free = 0.4433 target = 0.210690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.187641 restraints weight = 3084.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4153 rms_B_bonded: 5.39
r_work: 0.3970 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027    605  Z= 0.103
  Angle     :  0.636   7.085    810  Z= 0.294
  Chirality :  0.049   0.118     90
  Planarity :  0.005   0.042    104
  Dihedral  :  5.329  20.320     83
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.59 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.78), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.59), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 330 
 PHE   0.001   0.000   PHE A 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.7510 (pttm) cc_final: 0.7239 (ptmm)
REVERT: A  369 LYS cc_start: 0.7681 (ptmt) cc_final: 0.6656 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 19
  average time/residue: 1.5543
  time to fit residues: 29.7485
Evaluate side-chains
  19 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.5317

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.206231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.183370 restraints weight = 4252.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 5.94
r_work: 0.3906 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3896 r_free = 0.3896    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3896 r_free = 0.3896    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039    605  Z= 0.152
  Angle     :  0.728   7.421    810  Z= 0.342
  Chirality :  0.054   0.157     90
  Planarity :  0.005   0.047    104
  Dihedral  :  5.271  13.087     81
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.59 %
    Favored  : 77.94 %
  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: -2.02 (0.77), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.59), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.002   0.001   ARG A 379 

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

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

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  156 Ramachandran restraints generated.
    78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.7853 (ptmt) cc_final: 0.6703 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 1.4705
  time to fit residues: 20.7762
Evaluate side-chains
  14 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    2.8320

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.206136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.183816 restraints weight = 3931.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 5.82
r_work: 0.3914 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3906 r_free = 0.3906    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3906 r_free = 0.3906    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042    605  Z= 0.161
  Angle     :  0.743   7.245    810  Z= 0.353
  Chirality :  0.055   0.162     90
  Planarity :  0.006   0.047    104
  Dihedral  :  5.415  13.474     81
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 22.06 %
    Favored  : 76.47 %
  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 (0.76), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.58), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.003   0.001   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1182.39 seconds
wall clock time: 21 minutes 39.29 seconds (1299.29 seconds total)