Starting phenix.real_space_refine
on Fri Aug 22 13:57:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ore_17121/08_2025/8ore_17121.map"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    1110      2.51       5
     N     327      2.21       5
     O     330      1.98       5
     H    1845      0.53       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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3615
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1205
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1205
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1205
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Time building chain proxies: 0.72, per 1000 atoms: 0.20
  Number of scatterers: 3615
  At special positions: 0
  Unit cell: (82.84, 81.75, 37.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       3     16.00
     O     330      8.00
     N     327      7.00
     C    1110      6.00
     H    1845      1.00
    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: 0.18
  Conformation dependent library (CDL) restraints added in 81.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  402

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 49.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
    Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.612A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE B 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 361
      removed outlier: 6.938A  pdb=" N   SER B 352 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LYS A 353 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ILE B 354 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLY A 355 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   SER C 352 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LYS B 353 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE C 354 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLY B 355 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377

    62 hydrogen bonds defined for protein.
    186 hydrogen bond angles 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: 0.76

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 1842
        1.11 -     1.29: 297
        1.29 -     1.46: 490
        1.46 -     1.63: 1010
        1.63 -     1.81: 3
  Bond restraints: 3642
  Sorted by residual:
  bond pdb=" N   GLY A 366 "
       pdb=" H   GLY A 366 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE1 HIS A 362 "
       pdb=" HE1 HIS A 362 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" CE1 HIS B 362 "
       pdb=" HE1 HIS B 362 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   LEU C 315 "
       pdb=" H   LEU C 315 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   LEU B 315 "
       pdb=" H   LEU B 315 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 3637 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 5360
        2.37 -     4.75: 912
        4.75 -     7.12: 334
        7.12 -     9.50: 32
        9.50 -    11.87: 4
  Bond angle restraints: 6642
  Sorted by residual:
  angle pdb=" C   LEU A 325 "
        pdb=" CA  LEU A 325 "
        pdb=" CB  LEU A 325 "
      ideal   model   delta    sigma   weight residual
     111.14  119.05   -7.91 1.39e+00 5.18e-01 3.24e+01
  angle pdb=" C   LEU B 325 "
        pdb=" CA  LEU B 325 "
        pdb=" CB  LEU B 325 "
      ideal   model   delta    sigma   weight residual
     111.40  118.42   -7.02 1.29e+00 6.01e-01 2.96e+01
  angle pdb=" N   PRO B 364 "
        pdb=" CA  PRO B 364 "
        pdb=" C   PRO B 364 "
      ideal   model   delta    sigma   weight residual
     113.57  120.57   -7.00 1.31e+00 5.83e-01 2.86e+01
  angle pdb=" CB  HIS B 362 "
        pdb=" CG  HIS B 362 "
        pdb=" CD2 HIS B 362 "
      ideal   model   delta    sigma   weight residual
     131.20  124.91    6.29 1.30e+00 5.92e-01 2.34e+01
  angle pdb=" CA  PHE B 346 "
        pdb=" CB  PHE B 346 "
        pdb=" CG  PHE B 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.61   -4.81 1.00e+00 1.00e+00 2.31e+01
  ... (remaining 6637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    13.53: 1439
       13.53 -    27.06: 117
       27.06 -    40.59: 35
       40.59 -    54.12: 28
       54.12 -    67.65: 52
  Dihedral angle restraints: 1671
    sinusoidal: 960
      harmonic: 711
  Sorted by residual:
  dihedral pdb=" C   LEU A 325 "
           pdb=" N   LEU A 325 "
           pdb=" CA  LEU A 325 "
           pdb=" CB  LEU A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.99   16.39     0      2.50e+00 1.60e-01 4.30e+01
  dihedral pdb=" C   VAL B 363 "
           pdb=" N   VAL B 363 "
           pdb=" CA  VAL B 363 "
           pdb=" CB  VAL B 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.70   15.70     0      2.50e+00 1.60e-01 3.94e+01
  dihedral pdb=" C   VAL A 363 "
           pdb=" N   VAL A 363 "
           pdb=" CA  VAL A 363 "
           pdb=" CB  VAL A 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.54   14.54     0      2.50e+00 1.60e-01 3.38e+01
  ... (remaining 1668 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 200
       0.120 -    0.240: 40
       0.240 -    0.360: 16
       0.360 -    0.479: 9
       0.479 -    0.599: 2
  Chirality restraints: 267
  Sorted by residual:
  chirality pdb=" CA  LEU A 325 "
            pdb=" N   LEU A 325 "
            pdb=" C   LEU A 325 "
            pdb=" CB  LEU A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.97e+00
  chirality pdb=" CA  PRO B 364 "
            pdb=" N   PRO B 364 "
            pdb=" C   PRO B 364 "
            pdb=" CB  PRO B 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.23    0.49 2.00e-01 2.50e+01 5.94e+00
  chirality pdb=" CA  VAL B 363 "
            pdb=" N   VAL B 363 "
            pdb=" C   VAL B 363 "
            pdb=" CB  VAL B 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.21e+00
  ... (remaining 264 not shown)

  Planarity restraints: 525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 346 "    0.099 2.00e-02 2.50e+03   4.00e-02 4.80e+01
        pdb=" CG  PHE A 346 "    0.000 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 346 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 346 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 346 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 346 "    0.013 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 346 "   -0.050 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 346 "   -0.037 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 346 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 346 "    0.008 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 346 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 346 "    0.076 2.00e-02 2.50e+03   3.28e-02 3.23e+01
        pdb=" CG  PHE B 346 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 346 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 346 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 346 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 346 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 346 "   -0.043 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 346 "   -0.032 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 346 "    0.012 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 346 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 341 "   -0.030 2.00e-02 2.50e+03   5.52e-02 3.05e+01
        pdb=" N   GLU B 342 "    0.095 2.00e-02 2.50e+03
        pdb=" CA  GLU B 342 "   -0.027 2.00e-02 2.50e+03
        pdb=" H   GLU B 342 "   -0.038 2.00e-02 2.50e+03
  ... (remaining 522 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 317
        2.21 -     2.81: 6754
        2.81 -     3.40: 9317
        3.40 -     4.00: 12465
        4.00 -     4.60: 17899
  Nonbonded interactions: 46752
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" HG1 THR A 377 "
            pdb=" OE1 GLU A 380 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" HG1 THR C 377 "
            pdb=" OE2 GLU C 380 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.675 2.450
  ... (remaining 46747 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.080
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.180
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
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      :  0.011   0.052   1797  Z= 0.684
  Angle     :  2.085  10.566   2400  Z= 1.353
  Chirality :  0.140   0.599    267
  Planarity :  0.011   0.065    306
  Dihedral  : 10.934  54.560    696
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Cbeta Deviations :  3.48 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.040   0.012   TYR B 310 
 PHE   0.055   0.024   PHE B 378 
 HIS   0.011   0.003   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01092 ( 1797)
  covalent geometry    : angle       2.08517 ( 2400)
  hydrogen bonds       : bond        0.12146 (   62)
  hydrogen bonds       : angle       7.92576 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8330 (t0) cc_final: 0.8073 (t0)
REVERT: A  349 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7794 (ttp-110)
REVERT: B  314 ASP cc_start: 0.8198 (t0) cc_final: 0.7914 (t0)
REVERT: B  317 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7384 (ptpp)
REVERT: B  347 LYS cc_start: 0.8635 (mttt) cc_final: 0.8389 (mttp)
REVERT: C  307 GLN cc_start: 0.7873 (tt0) cc_final: 0.7448 (tt0)
REVERT: C  338 GLU cc_start: 0.8150 (tt0) cc_final: 0.7887 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 1.0928
  time to fit residues: 90.7270
Evaluate side-chains
  52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
A 368 ASN
A 374 HIS
B 307 GLN
B 336 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.147503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.127031 restraints weight = 6096.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.00
r_work: 0.3910 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1797  Z= 0.128
  Angle     :  0.712   4.862   2400  Z= 0.369
  Chirality :  0.055   0.147    267
  Planarity :  0.005   0.041    306
  Dihedral  :  7.240  22.117    237
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 20.40 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.47), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 349 
 TYR   0.006   0.002   TYR B 310 
 PHE   0.012   0.002   PHE A 378 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 1797)
  covalent geometry    : angle       0.71167 ( 2400)
  hydrogen bonds       : bond        0.03094 (   62)
  hydrogen bonds       : angle       6.00355 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8138 (t0) cc_final: 0.7819 (t0)
REVERT: A  372 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6435 (mt-10)
REVERT: B  314 ASP cc_start: 0.8617 (t0) cc_final: 0.8390 (t0)
REVERT: B  317 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8097 (ptpp)
REVERT: B  319 THR cc_start: 0.8624 (m) cc_final: 0.8257 (p)
REVERT: B  347 LYS cc_start: 0.8068 (mttt) cc_final: 0.7776 (mttp)
REVERT: C  307 GLN cc_start: 0.8480 (tt0) cc_final: 0.8276 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 66
  average time/residue: 1.0195
  time to fit residues: 68.3849
Evaluate side-chains
  48 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.148049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.128874 restraints weight = 6104.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 1.99
r_work: 0.3916 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3824 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.5385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1797  Z= 0.110
  Angle     :  0.616   4.741   2400  Z= 0.312
  Chirality :  0.053   0.137    267
  Planarity :  0.004   0.037    306
  Dihedral  :  6.177  18.289    237
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.88 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.47), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 349 
 TYR   0.006   0.001   TYR C 310 
 PHE   0.010   0.002   PHE A 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 1797)
  covalent geometry    : angle       0.61612 ( 2400)
  hydrogen bonds       : bond        0.02433 (   62)
  hydrogen bonds       : angle       5.21846 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8144 (t0) cc_final: 0.7862 (t0)
REVERT: A  359 ASN cc_start: 0.8980 (m-40) cc_final: 0.8767 (m-40)
REVERT: B  319 THR cc_start: 0.8555 (m) cc_final: 0.8220 (p)
REVERT: B  345 ASP cc_start: 0.7610 (t0) cc_final: 0.7185 (t70)
REVERT: C  307 GLN cc_start: 0.8387 (tt0) cc_final: 0.8187 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 51
  average time/residue: 0.9852
  time to fit residues: 51.1923
Evaluate side-chains
  52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 9 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
B 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.149918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.130387 restraints weight = 6066.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.94
r_work: 0.3958 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3866 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1797  Z= 0.096
  Angle     :  0.577   3.966   2400  Z= 0.288
  Chirality :  0.052   0.132    267
  Planarity :  0.003   0.032    306
  Dihedral  :  5.711  17.617    237
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.89 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.47), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 349 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.008   0.002   PHE C 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 1797)
  covalent geometry    : angle       0.57726 ( 2400)
  hydrogen bonds       : bond        0.02010 (   62)
  hydrogen bonds       : angle       4.74649 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8184 (t0) cc_final: 0.7886 (t0)
REVERT: B  319 THR cc_start: 0.8574 (m) cc_final: 0.8253 (p)
REVERT: B  345 ASP cc_start: 0.7610 (t0) cc_final: 0.7150 (t70)
REVERT: C  307 GLN cc_start: 0.8385 (tt0) cc_final: 0.8166 (tt0)
REVERT: C  336 GLN cc_start: 0.8467 (tt0) cc_final: 0.8201 (mt0)
REVERT: C  380 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6541 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 53
  average time/residue: 0.9063
  time to fit residues: 48.8974
Evaluate side-chains
  52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.145152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.125344 restraints weight = 6168.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.06
r_work: 0.3874 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.5994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1797  Z= 0.121
  Angle     :  0.583   4.500   2400  Z= 0.293
  Chirality :  0.052   0.142    267
  Planarity :  0.004   0.038    306
  Dihedral  :  5.658  18.231    237
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.88 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 349 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.012   0.002   PHE A 378 
 HIS   0.003   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 1797)
  covalent geometry    : angle       0.58311 ( 2400)
  hydrogen bonds       : bond        0.02168 (   62)
  hydrogen bonds       : angle       4.68626 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8116 (t0) cc_final: 0.7816 (t0)
REVERT: A  372 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7119 (tt0)
REVERT: B  319 THR cc_start: 0.8585 (m) cc_final: 0.8274 (p)
REVERT: B  345 ASP cc_start: 0.7601 (t0) cc_final: 0.7052 (t70)
REVERT: C  307 GLN cc_start: 0.8362 (tt0) cc_final: 0.8152 (tt0)
REVERT: C  336 GLN cc_start: 0.8504 (tt0) cc_final: 0.8267 (mt0)
REVERT: C  345 ASP cc_start: 0.7893 (t0) cc_final: 0.7410 (t70)
REVERT: C  349 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7038 (mtp180)
  outliers start: 9
  outliers final: 5
  residues processed: 51
  average time/residue: 0.9667
  time to fit residues: 50.1406
Evaluate side-chains
  53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.147268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.128248 restraints weight = 6198.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 2.01
r_work: 0.3916 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3825 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.6144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   1797  Z= 0.104
  Angle     :  0.576   4.227   2400  Z= 0.284
  Chirality :  0.051   0.126    267
  Planarity :  0.003   0.032    306
  Dihedral  :  5.397  18.383    237
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.88 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.47), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.007   0.001   PHE C 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 1797)
  covalent geometry    : angle       0.57616 ( 2400)
  hydrogen bonds       : bond        0.01947 (   62)
  hydrogen bonds       : angle       4.49258 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8331 (tttp)
REVERT: A  345 ASP cc_start: 0.8134 (t0) cc_final: 0.7849 (t0)
REVERT: A  372 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6997 (tt0)
REVERT: A  380 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6738 (mt-10)
REVERT: B  319 THR cc_start: 0.8579 (m) cc_final: 0.8289 (p)
REVERT: B  345 ASP cc_start: 0.7606 (t0) cc_final: 0.7045 (t70)
REVERT: C  307 GLN cc_start: 0.8302 (tt0) cc_final: 0.8064 (tt0)
REVERT: C  336 GLN cc_start: 0.8505 (tt0) cc_final: 0.8263 (mt0)
REVERT: C  345 ASP cc_start: 0.7907 (t0) cc_final: 0.7405 (t70)
REVERT: C  349 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7075 (mtp180)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 1.0007
  time to fit residues: 53.9898
Evaluate side-chains
  56 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.143506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.124025 restraints weight = 6290.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.05
r_work: 0.3852 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.6162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1797  Z= 0.125
  Angle     :  0.592   4.410   2400  Z= 0.295
  Chirality :  0.052   0.145    267
  Planarity :  0.004   0.036    306
  Dihedral  :  5.443  19.270    237
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.88 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.009   0.002   PHE C 378 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 1797)
  covalent geometry    : angle       0.59207 ( 2400)
  hydrogen bonds       : bond        0.02048 (   62)
  hydrogen bonds       : angle       4.51499 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8335 (tttp)
REVERT: A  345 ASP cc_start: 0.8126 (t0) cc_final: 0.7833 (t0)
REVERT: B  315 LEU cc_start: 0.9075 (mp) cc_final: 0.8850 (mm)
REVERT: B  319 THR cc_start: 0.8597 (m) cc_final: 0.8302 (p)
REVERT: B  345 ASP cc_start: 0.7613 (t0) cc_final: 0.7065 (t70)
REVERT: B  373 THR cc_start: 0.8771 (p) cc_final: 0.8563 (p)
REVERT: C  336 GLN cc_start: 0.8570 (tt0) cc_final: 0.8338 (mt0)
REVERT: C  345 ASP cc_start: 0.7923 (t0) cc_final: 0.7405 (t70)
REVERT: C  349 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7001 (mtp180)
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 1.1489
  time to fit residues: 61.9577
Evaluate side-chains
  54 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.146744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.127233 restraints weight = 6256.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 2.07
r_work: 0.3902 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.6255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   1797  Z= 0.102
  Angle     :  0.585   4.685   2400  Z= 0.289
  Chirality :  0.051   0.125    267
  Planarity :  0.003   0.032    306
  Dihedral  :  5.275  18.503    237
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 25.87 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.47), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.005   0.001   PHE C 378 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 1797)
  covalent geometry    : angle       0.58489 ( 2400)
  hydrogen bonds       : bond        0.01956 (   62)
  hydrogen bonds       : angle       4.37590 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7830 (tttm)
REVERT: A  343 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8314 (tttp)
REVERT: A  345 ASP cc_start: 0.8122 (t0) cc_final: 0.7841 (t0)
REVERT: B  315 LEU cc_start: 0.9070 (mp) cc_final: 0.8841 (mm)
REVERT: B  319 THR cc_start: 0.8572 (m) cc_final: 0.8289 (p)
REVERT: B  345 ASP cc_start: 0.7583 (t0) cc_final: 0.7034 (t70)
REVERT: B  373 THR cc_start: 0.8803 (p) cc_final: 0.8583 (p)
REVERT: C  336 GLN cc_start: 0.8534 (tt0) cc_final: 0.8304 (mt0)
REVERT: C  345 ASP cc_start: 0.7915 (t0) cc_final: 0.7415 (t70)
REVERT: C  349 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.6986 (mtp180)
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 1.1075
  time to fit residues: 59.6875
Evaluate side-chains
  56 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.144063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.123557 restraints weight = 6131.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.06
r_work: 0.3868 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.6294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   1797  Z= 0.131
  Angle     :  0.624   4.414   2400  Z= 0.309
  Chirality :  0.052   0.137    267
  Planarity :  0.003   0.035    306
  Dihedral  :  5.278  18.049    237
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.36 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.007   0.001   PHE C 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 1797)
  covalent geometry    : angle       0.62425 ( 2400)
  hydrogen bonds       : bond        0.02131 (   62)
  hydrogen bonds       : angle       4.45456 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (tttp)
REVERT: A  345 ASP cc_start: 0.8132 (t0) cc_final: 0.7832 (t0)
REVERT: B  315 LEU cc_start: 0.9057 (mp) cc_final: 0.8844 (mm)
REVERT: B  319 THR cc_start: 0.8578 (m) cc_final: 0.8292 (p)
REVERT: B  345 ASP cc_start: 0.7572 (t0) cc_final: 0.7024 (t70)
REVERT: B  373 THR cc_start: 0.8834 (p) cc_final: 0.8576 (p)
REVERT: C  336 GLN cc_start: 0.8551 (tt0) cc_final: 0.8314 (mt0)
REVERT: C  345 ASP cc_start: 0.7939 (t0) cc_final: 0.7441 (t70)
REVERT: C  349 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6946 (mtp180)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 1.1144
  time to fit residues: 55.5827
Evaluate side-chains
  51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0020
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.150616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.133110 restraints weight = 6798.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.07
r_work: 0.4012 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.6441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   1797  Z= 0.100
  Angle     :  0.590   4.447   2400  Z= 0.288
  Chirality :  0.051   0.125    267
  Planarity :  0.003   0.031    306
  Dihedral  :  4.961  16.234    237
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 27.36 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.003   0.001   TYR C 310 
 PHE   0.005   0.001   PHE B 378 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 1797)
  covalent geometry    : angle       0.59019 ( 2400)
  hydrogen bonds       : bond        0.01746 (   62)
  hydrogen bonds       : angle       4.22916 (  186)

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

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

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  450 Ramachandran restraints generated.
    225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8288 (tttp)
REVERT: B  315 LEU cc_start: 0.9059 (mp) cc_final: 0.8855 (mm)
REVERT: B  319 THR cc_start: 0.8588 (m) cc_final: 0.8335 (p)
REVERT: B  345 ASP cc_start: 0.7563 (t0) cc_final: 0.6993 (t70)
REVERT: B  373 THR cc_start: 0.8816 (p) cc_final: 0.8570 (p)
REVERT: C  336 GLN cc_start: 0.8525 (tt0) cc_final: 0.8301 (mt0)
REVERT: C  345 ASP cc_start: 0.7837 (t0) cc_final: 0.7348 (t70)
REVERT: C  349 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6974 (mtp180)
  outliers start: 5
  outliers final: 2
  residues processed: 49
  average time/residue: 1.1443
  time to fit residues: 57.0148
Evaluate side-chains
  51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.150494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.131214 restraints weight = 6174.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.09
r_work: 0.3985 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3895 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.6500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   1797  Z= 0.114
  Angle     :  0.621   4.414   2400  Z= 0.303
  Chirality :  0.052   0.127    267
  Planarity :  0.003   0.032    306
  Dihedral  :  5.031  17.050    237
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 28.36 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.48), residues: 225
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 349 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.006   0.001   PHE C 378 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 1797)
  covalent geometry    : angle       0.62129 ( 2400)
  hydrogen bonds       : bond        0.01862 (   62)
  hydrogen bonds       : angle       4.29928 (  186)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2239.12 seconds
wall clock time: 38 minutes 40.49 seconds (2320.49 seconds total)