Starting phenix.real_space_refine
on Wed Mar  5 14:16:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eo7_19846/03_2025/9eo7_19846.cif"
  }
  resolution = 2.8
  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       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 7 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: 1.13, per 1000 atoms: 1.90
  Number of scatterers: 595
  At special positions: 0
  Unit cell: (70.864, 84.048, 23.072, 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 152.4 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: 0.45
  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: 0.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 154
        1.34 -     1.46: 145
        1.46 -     1.58: 303
        1.58 -     1.70: 0
        1.70 -     1.82: 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  1.406 -0.075 1.27e-02 6.20e+03 3.52e+01
  bond pdb=" CG  HIS A 330 "
       pdb=" CD2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.296  0.058 1.10e-02 8.26e+03 2.75e+01
  bond pdb=" CG  HIS A 362 "
       pdb=" CD2 HIS A 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.300  0.054 1.10e-02 8.26e+03 2.37e+01
  bond pdb=" CA  SER A 316 "
       pdb=" CB  SER A 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.485  0.044 1.66e-02 3.63e+03 7.04e+00
  bond pdb=" CE1 HIS A 330 "
       pdb=" NE2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.321  1.295  0.026 1.00e-02 1.00e+04 6.66e+00
  ... (remaining 600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 624
        1.67 -     3.34: 145
        3.34 -     5.01: 33
        5.01 -     6.68: 6
        6.68 -     8.35: 2
  Bond angle restraints: 810
  Sorted by residual:
  angle pdb=" C   ARG A 349 "
        pdb=" CA  ARG A 349 "
        pdb=" CB  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     111.73  120.08   -8.35 1.42e+00 4.96e-01 3.46e+01
  angle pdb=" CB  HIS A 330 "
        pdb=" CG  HIS A 330 "
        pdb=" CD2 HIS A 330 "
      ideal   model   delta    sigma   weight residual
     131.20  125.05    6.15 1.30e+00 5.92e-01 2.24e+01
  angle pdb=" CB  HIS A 330 "
        pdb=" CG  HIS A 330 "
        pdb=" ND1 HIS A 330 "
      ideal   model   delta    sigma   weight residual
     122.70  129.39   -6.69 1.50e+00 4.44e-01 1.99e+01
  angle pdb=" CA  THR A 361 "
        pdb=" CB  THR A 361 "
        pdb=" OG1 THR A 361 "
      ideal   model   delta    sigma   weight residual
     109.60  103.04    6.56 1.50e+00 4.44e-01 1.91e+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  115.84   -5.15 1.33e+00 5.65e-01 1.50e+01
  ... (remaining 805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.86: 263
        7.86 -    15.71: 70
       15.71 -    23.57: 20
       23.57 -    31.43: 12
       31.43 -    39.28: 5
  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 -135.14   12.54     0      2.50e+00 1.60e-01 2.52e+01
  dihedral pdb=" CA  SER A 352 "
           pdb=" C   SER A 352 "
           pdb=" N   LYS A 353 "
           pdb=" CA  LYS A 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.32   21.68     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  ARG A 379 "
           pdb=" C   ARG A 379 "
           pdb=" N   GLU A 380 "
           pdb=" CA  GLU A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.51   21.49     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.077: 46
       0.077 -    0.151: 36
       0.151 -    0.226: 7
       0.226 -    0.300: 0
       0.300 -    0.375: 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    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" CA AMET A 337 "
            pdb=" N  AMET A 337 "
            pdb=" C  AMET A 337 "
            pdb=" CB AMET A 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ASP A 358 "
            pdb=" N   ASP A 358 "
            pdb=" C   ASP A 358 "
            pdb=" CB  ASP A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 87 not shown)

  Planarity restraints: 104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 336 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.45e+00
        pdb=" C   GLN A 336 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLN A 336 "   -0.018 2.00e-02 2.50e+03
        pdb=" N  BVAL A 337 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 349 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.03e+00
        pdb=" C   ARG A 349 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ARG A 349 "   -0.016 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=" CB  TYR A 310 "    0.028 2.00e-02 2.50e+03   1.70e-02 5.75e+00
        pdb=" CG  TYR A 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.004 2.00e-02 2.50e+03
  ... (remaining 101 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.05: 308
        3.05 -     3.51: 481
        3.51 -     3.97: 687
        3.97 -     4.44: 515
        4.44 -     4.90: 1012
  Nonbonded interactions: 3003
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.583 3.040
  nonbonded pdb=" O   GLY A 334 "
            pdb=" CA  GLY A 335 "
     model   vdw
     2.662 2.752
  nonbonded pdb=" OD2 ASP A 314 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.667 3.120
  nonbonded pdb=" N   ASN A 368 "
            pdb=" O   ASN A 368 "
     model   vdw
     2.668 2.496
  nonbonded pdb=" O   LEU A 325 "
            pdb=" CA  GLY A 326 "
     model   vdw
     2.674 2.752
  ... (remaining 2998 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:             2.740
  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:                     8.540
  Find NCS groups from input model:        0.000
  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:13.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
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   0.075    605  Z= 0.670
  Angle     :  1.590   8.348    810  Z= 1.025
  Chirality :  0.095   0.375     90
  Planarity :  0.009   0.032    104
  Dihedral  : 12.220  39.283    234
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  8.82 %
    Favored  : 89.71 %
  Cbeta Deviations :  1.47 %
  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: -4.16 (0.58), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.44), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS A 330 
 PHE   0.032   0.008   PHE A 346 
 TYR   0.038   0.011   TYR A 310 
 ARG   0.004   0.001   ARG A 379 

*********************** 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
  17 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.053 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8399 (ttpt)
REVERT: A  343 LYS cc_start: 0.8476 (mttp) cc_final: 0.8072 (mtpp)
REVERT: A  349 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7588 (ptm160)
REVERT: A  375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7950 (ttmp)
  outliers start: 1
  outliers final: 0
  residues processed: 17
  average time/residue: 1.2030
  time to fit residues: 20.6451
Evaluate side-chains
  12 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4310

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 330 HIS
A 368 ASN
A 374 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.206512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.183923 restraints weight = 6035.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.4409 rms_B_bonded: 6.38
r_work: 0.4223 rms_B_bonded: 5.47 restraints_weight: 2.0000
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4250 r_free = 0.4250    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4262 r_free = 0.4262    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016    605  Z= 0.104
  Angle     :  0.540   5.057    810  Z= 0.273
  Chirality :  0.049   0.129     90
  Planarity :  0.004   0.025    104
  Dihedral  :  5.179  13.747     81
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.18 %
    Favored  : 83.82 %
  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: -3.01 (0.73), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.56), residues: 78

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

*********************** 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
  12 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8420 (mttp) cc_final: 0.8031 (mtpp)
REVERT: A  348 ASP cc_start: 0.8541 (t0) cc_final: 0.7774 (m-30)
REVERT: A  358 ASP cc_start: 0.8488 (p0) cc_final: 0.8099 (m-30)
REVERT: A  375 LYS cc_start: 0.8204 (tttt) cc_final: 0.7836 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 1.3877
  time to fit residues: 16.8270
Evaluate side-chains
  8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    3.3323

-------------------------------------------------------------------------------
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 = 0.4502 r_free = 0.4502 target = 0.171141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.153033 restraints weight = 977.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 2.74
r_work: 0.4208 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4124 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4113 r_free = 0.4113    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4112 r_free = 0.4112    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029    605  Z= 0.221
  Angle     :  0.626   5.447    810  Z= 0.322
  Chirality :  0.050   0.148     90
  Planarity :  0.005   0.035    104
  Dihedral  :  5.209  12.982     81
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.71 %
    Favored  : 82.35 %
  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: -2.50 (0.77), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.58), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.013   0.004   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

*********************** 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
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.067 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 7
  average time/residue: 0.7337
  time to fit residues: 5.2835
Evaluate side-chains
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  358 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.6657

-------------------------------------------------------------------------------
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 = 0.4468 r_free = 0.4468 target = 0.166185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.146146 restraints weight = 3312.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.4241 rms_B_bonded: 4.46
r_work: 0.4101 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030    605  Z= 0.238
  Angle     :  0.685   8.099    810  Z= 0.333
  Chirality :  0.051   0.146     90
  Planarity :  0.005   0.037    104
  Dihedral  :  5.181  12.492     81
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 16.18 %
    Favored  : 79.41 %
  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 (0.82), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.62), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 330 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.015   0.004   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

*********************** 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
  11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 8
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5187 (mp0)
REVERT: A  379 ARG cc_start: 0.8593 (mpt-90) cc_final: 0.6510 (pmt170)
  outliers start: 3
  outliers final: 2
  residues processed: 10
  average time/residue: 0.8736
  time to fit residues: 8.9013
Evaluate side-chains
  11 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 8
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    2.4320

-------------------------------------------------------------------------------
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 = 0.4482 r_free = 0.4482 target = 0.167706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.147047 restraints weight = 4121.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.4260 rms_B_bonded: 4.86
r_work: 0.4110 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4098 r_free = 0.4098    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4098 r_free = 0.4098    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026    605  Z= 0.168
  Angle     :  0.612   7.675    810  Z= 0.294
  Chirality :  0.050   0.140     90
  Planarity :  0.004   0.037    104
  Dihedral  :  4.965  11.889     81
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.12 %
    Favored  : 79.41 %
  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 (0.84), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.011   0.003   TYR A 310 
 ARG   0.001   0.000   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
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 8
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5182 (mp0)
REVERT: A  379 ARG cc_start: 0.8582 (mpt-90) cc_final: 0.6525 (pmt170)
  outliers start: 1
  outliers final: 1
  residues processed: 9
  average time/residue: 1.2358
  time to fit residues: 11.2884
Evaluate side-chains
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0670
   overall best weight:    2.3550

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.168037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.146939 restraints weight = 5833.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 5.39
r_work: 0.4105 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4092 r_free = 0.4092    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4092 r_free = 0.4092    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024    605  Z= 0.164
  Angle     :  0.616   7.803    810  Z= 0.298
  Chirality :  0.049   0.138     90
  Planarity :  0.005   0.043    104
  Dihedral  :  4.897  11.782     81
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.65 %
    Favored  : 79.41 %
  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 (0.83), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.011   0.003   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
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5397 (mp0)
REVERT: A  379 ARG cc_start: 0.8593 (mpt-90) cc_final: 0.6577 (pmt170)
  outliers start: 2
  outliers final: 1
  residues processed: 8
  average time/residue: 1.3338
  time to fit residues: 10.8721
Evaluate side-chains
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  342 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3323

-------------------------------------------------------------------------------
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 = 0.4542 r_free = 0.4542 target = 0.172236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.153465 restraints weight = 6556.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 5.26
r_work: 0.4188 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019    605  Z= 0.113
  Angle     :  0.568   7.760    810  Z= 0.271
  Chirality :  0.049   0.129     90
  Planarity :  0.005   0.046    104
  Dihedral  :  4.514  10.551     81
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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: -2.05 (0.84), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.001   0.000   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
  9 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  379 ARG cc_start: 0.8572 (mpt-90) cc_final: 0.6514 (pmt170)
  outliers start: 2
  outliers final: 1
  residues processed: 9
  average time/residue: 1.0074
  time to fit residues: 9.2225
Evaluate side-chains
  8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 7
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8983

-------------------------------------------------------------------------------
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 = 0.4566 r_free = 0.4566 target = 0.197837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.176620 restraints weight = 3003.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.4380 rms_B_bonded: 4.47
r_work: 0.4246 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4227 r_free = 0.4227    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4227 r_free = 0.4227    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015    605  Z= 0.097
  Angle     :  0.571   8.463    810  Z= 0.266
  Chirality :  0.049   0.125     90
  Planarity :  0.005   0.048    104
  Dihedral  :  4.265  10.446     81
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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: -2.04 (0.83), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.002   0.000   PHE A 346 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.001   0.000   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
  8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 7
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8364 (t0) cc_final: 0.7914 (m-30)
REVERT: A  379 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.6543 (ppt170)
  outliers start: 1
  outliers final: 1
  residues processed: 8
  average time/residue: 0.8256
  time to fit residues: 6.7629
Evaluate side-chains
  8 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 7
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.2650

-------------------------------------------------------------------------------
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 = 0.4553 r_free = 0.4553 target = 0.196201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.174622 restraints weight = 4122.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 5.00
r_work: 0.4212 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018    605  Z= 0.111
  Angle     :  0.578   8.551    810  Z= 0.270
  Chirality :  0.049   0.129     90
  Planarity :  0.006   0.052    104
  Dihedral  :  4.314  10.069     81
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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: -2.01 (0.84), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.008   0.002   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
  10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7929 (m-30)
REVERT: A  379 ARG cc_start: 0.8573 (mpt-90) cc_final: 0.6535 (ppt170)
  outliers start: 2
  outliers final: 1
  residues processed: 8
  average time/residue: 0.8345
  time to fit residues: 6.8256
Evaluate side-chains
  10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0000
   overall best weight:    1.5323

-------------------------------------------------------------------------------
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 = 0.4546 r_free = 0.4546 target = 0.195451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.173821 restraints weight = 5377.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.4354 rms_B_bonded: 5.41
r_work: 0.4192 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4170 r_free = 0.4170    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4170 r_free = 0.4170    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019    605  Z= 0.123
  Angle     :  0.587   8.607    810  Z= 0.276
  Chirality :  0.049   0.132     90
  Planarity :  0.006   0.053    104
  Dihedral  :  4.383  10.177     81
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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: -2.05 (0.84), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.001   0.000   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
  10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7808 (m-30)
REVERT: A  379 ARG cc_start: 0.8577 (mpt-90) cc_final: 0.6569 (ppt170)
  outliers start: 2
  outliers final: 1
  residues processed: 8
  average time/residue: 0.8195
  time to fit residues: 6.7124
Evaluate side-chains
  10 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 7
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0020
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.4660

-------------------------------------------------------------------------------
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 = 0.4591 r_free = 0.4591 target = 0.201233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.181022 restraints weight = 5965.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.4414 rms_B_bonded: 6.07
r_work: 0.4240 rms_B_bonded: 5.00 restraints_weight: 2.0000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4224 r_free = 0.4224    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4224 r_free = 0.4224    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019    605  Z= 0.087
  Angle     :  0.552   8.574    810  Z= 0.254
  Chirality :  0.049   0.121     90
  Planarity :  0.005   0.051    104
  Dihedral  :  4.066  10.814     81
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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: -1.99 (0.84), residues: 78
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 362 
 PHE   0.001   0.000   PHE A 346 
 TYR   0.003   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1001.86 seconds
wall clock time: 18 minutes 43.66 seconds (1123.66 seconds total)