Starting phenix.real_space_refine
on Fri Aug 22 12:36:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v85_43023/08_2025/8v85_43023.map"
  }
  resolution = 2.9
  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=   0.001
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       8      5.16       5
     C     986      2.51       5
     N     268      2.21       5
     O     277      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 1539
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "3"
      Number of atoms: 1539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1539
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 10, 'TRANS': 186}
  Time building chain proxies: 0.67, per 1000 atoms: 0.44
  Number of scatterers: 1539
  At special positions: 0
  Unit cell: (59.4, 59.4, 52.92, 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       8     16.00
     O     277      8.00
     N     268      7.00
     C     986      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: 0.13
  Conformation dependent library (CDL) restraints added in 39.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  368

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 1 sheets defined
      57.9% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing helix  chain '3' and resid 146 through 155
    Processing helix  chain '3' and resid 161 through 173
      Proline residue:  3 169  - end of helix
    Processing helix  chain '3' and resid 188 through 199
      Proline residue:  3 194  - end of helix
    Processing helix  chain '3' and resid 216 through 232
    Processing helix  chain '3' and resid 246 through 256
    Processing helix  chain '3' and resid 264 through 276
    Processing helix  chain '3' and resid 278 through 282
      removed outlier: 4.164A  pdb=" N   SER 3 281 " --> pdb=" O   ASP 3 278 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 289 through 297
    Processing helix  chain '3' and resid 298 through 309
      removed outlier: 3.548A  pdb=" N   GLU 3 304 " --> pdb=" O   GLU 3 300 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 323 through 334
    Processing sheet with id=AA1, first strand: chain '3' and resid 238 through 241
      removed outlier: 6.138A  pdb=" N   VAL 3 239 " --> pdb=" O   ILE 3 262 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA 3 210 " --> pdb=" O   ILE 3 261 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ALA 3 263 " --> pdb=" O   ALA 3 210 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE 3 212 " --> pdb=" O   ALA 3 263 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL 3 211 " --> pdb=" O   VAL 3 286 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ASP 3 288 " --> pdb=" O   VAL 3 211 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU 3 213 " --> pdb=" O   ASP 3 288 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL 3 285 " --> pdb=" O   LEU 3 316 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   PHE 3 318 " --> pdb=" O   VAL 3 285 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   PHE 3 287 " --> pdb=" O   PHE 3 318 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE 3 177 " --> pdb=" O   THR 3 315 " (cutoff:3.500A)

    71 hydrogen bonds defined for protein.
    210 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: 0.15

  Time building geometry restraints manager: 0.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 506
        1.34 -     1.46: 262
        1.46 -     1.57: 779
        1.57 -     1.69: 0
        1.69 -     1.80: 16
  Bond restraints: 1563
  Sorted by residual:
  bond pdb=" CA  THR 3 312 "
       pdb=" CB  THR 3 312 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 1.32e-02 5.74e+03 3.59e-01
  bond pdb=" CA  THR 3 312 "
       pdb=" C   THR 3 312 "
    ideal  model  delta    sigma   weight residual
    1.530  1.524  0.006 1.10e-02 8.26e+03 2.91e-01
  bond pdb=" C   LYS 3 198 "
       pdb=" N   LEU 3 199 "
    ideal  model  delta    sigma   weight residual
    1.331  1.338 -0.007 1.25e-02 6.40e+03 2.85e-01
  bond pdb=" CA  ILE 3 168 "
       pdb=" C   ILE 3 168 "
    ideal  model  delta    sigma   weight residual
    1.520  1.524 -0.004 8.80e-03 1.29e+04 2.21e-01
  bond pdb=" CA  LEU 3 193 "
       pdb=" C   LEU 3 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.526 -0.006 1.23e-02 6.61e+03 2.01e-01
  ... (remaining 1558 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 2065
        1.33 -     2.66: 27
        2.66 -     3.98: 13
        3.98 -     5.31: 2
        5.31 -     6.64: 1
  Bond angle restraints: 2108
  Sorted by residual:
  angle pdb=" C   ALA 3 263 "
        pdb=" N   THR 3 264 "
        pdb=" CA  THR 3 264 "
      ideal   model   delta    sigma   weight residual
     120.94  127.58   -6.64 1.90e+00 2.77e-01 1.22e+01
  angle pdb=" N   GLY 3 244 "
        pdb=" CA  GLY 3 244 "
        pdb=" C   GLY 3 244 "
      ideal   model   delta    sigma   weight residual
     115.08  112.16    2.92 1.19e+00 7.06e-01 6.04e+00
  angle pdb=" CA  PHE 3 298 "
        pdb=" C   PHE 3 298 "
        pdb=" O   PHE 3 298 "
      ideal   model   delta    sigma   weight residual
     119.23  116.51    2.72 1.54e+00 4.22e-01 3.11e+00
  angle pdb=" CA  THR 3 312 "
        pdb=" C   THR 3 312 "
        pdb=" N   ARG 3 313 "
      ideal   model   delta    sigma   weight residual
     114.76  116.67   -1.91 1.14e+00 7.69e-01 2.80e+00
  angle pdb=" CA  THR 3 312 "
        pdb=" C   THR 3 312 "
        pdb=" O   THR 3 312 "
      ideal   model   delta    sigma   weight residual
     122.64  120.61    2.03 1.25e+00 6.40e-01 2.64e+00
  ... (remaining 2103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.18: 847
        9.18 -    18.35: 91
       18.35 -    27.53: 18
       27.53 -    36.71: 6
       36.71 -    45.88: 6
  Dihedral angle restraints: 968
    sinusoidal: 403
      harmonic: 565
  Sorted by residual:
  dihedral pdb=" N   LYS 3 155 "
           pdb=" CA  LYS 3 155 "
           pdb=" CB  LYS 3 155 "
           pdb=" CG  LYS 3 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -134.12  -45.88     3      1.50e+01 4.44e-03 8.24e+00
  dihedral pdb=" N   LYS 3 228 "
           pdb=" CA  LYS 3 228 "
           pdb=" CB  LYS 3 228 "
           pdb=" CG  LYS 3 228 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -103.18   43.18     3      1.50e+01 4.44e-03 7.76e+00
  dihedral pdb=" CA  ALA 3 263 "
           pdb=" C   ALA 3 263 "
           pdb=" N   THR 3 264 "
           pdb=" CA  THR 3 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.40   13.60     0      5.00e+00 4.00e-02 7.39e+00
  ... (remaining 965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.027: 162
       0.027 -    0.054: 49
       0.054 -    0.081: 19
       0.081 -    0.107: 13
       0.107 -    0.134: 8
  Chirality restraints: 251
  Sorted by residual:
  chirality pdb=" CA  ILE 3 261 "
            pdb=" N   ILE 3 261 "
            pdb=" C   ILE 3 261 "
            pdb=" CB  ILE 3 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  ILE 3 212 "
            pdb=" N   ILE 3 212 "
            pdb=" C   ILE 3 212 "
            pdb=" CB  ILE 3 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  VAL 3 178 "
            pdb=" N   VAL 3 178 "
            pdb=" C   VAL 3 178 "
            pdb=" CB  VAL 3 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 248 not shown)

  Planarity restraints: 269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR 3 161 "   -0.017 5.00e-02 4.00e+02   2.51e-02 1.01e+00
        pdb=" N   PRO 3 162 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO 3 162 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO 3 162 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE 3 168 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.62e-01
        pdb=" N   PRO 3 169 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO 3 169 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO 3 169 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE 3 191 "    0.006 2.00e-02 2.50e+03   5.13e-03 4.61e-01
        pdb=" CG  PHE 3 191 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE 3 191 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE 3 191 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE 3 191 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE 3 191 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE 3 191 "    0.001 2.00e-02 2.50e+03
  ... (remaining 266 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 499
        2.85 -     3.37: 1485
        3.37 -     3.88: 2523
        3.88 -     4.39: 2831
        4.39 -     4.90: 4700
  Nonbonded interactions: 12038
  Sorted by model distance:
  nonbonded pdb=" O   ASP 3 245 "
            pdb=" NH2 ARG 3 267 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" NH2 ARG 3 209 "
            pdb=" OD2 ASP 3 259 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OE1 GLN 3 250 "
            pdb=" NE  ARG 3 267 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" N   GLN 3 301 "
            pdb=" OE1 GLN 3 301 "
     model   vdw
     2.439 3.120
  nonbonded pdb=" O   ILE 3 163 "
            pdb=" OG1 THR 3 167 "
     model   vdw
     2.486 3.040
  ... (remaining 12033 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.330
  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:          0.020
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.110
  Find NCS groups from input model:        0.010
  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:5.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1091
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1563  Z= 0.101
  Angle     :  0.504   6.641   2108  Z= 0.280
  Chirality :  0.041   0.134    251
  Planarity :  0.003   0.025    269
  Dihedral  :  8.921  45.882    600
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  1.33 (0.61), residues: 195
  helix:  1.64 (0.52), residues: 108
  sheet:  0.27 (0.76), residues: 39
  loop : -0.15 (0.89), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG 3 341 
 TYR   0.006   0.001   TYR 3 284 
 PHE   0.012   0.001   PHE 3 191 
 HIS   0.001   0.000   HIS 3 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 1563)
  covalent geometry    : angle       0.50439 ( 2108)
  hydrogen bonds       : bond        0.04078 (   71)
  hydrogen bonds       : angle       4.15719 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.045 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.5164
  time to fit residues: 12.0549
Evaluate side-chains
  14 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 6 optimal weight:   30.0000
   chunk 4 optimal weight:    0.6980
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
3 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.120051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.104612 restraints weight = 269887.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.4826 rms_B_bonded: 69.45
r_work: 0.4427 rms_B_bonded: 50.99 restraints_weight: 2.0000
r_work: 0.4547 rms_B_bonded: 37.66 restraints_weight: 4.0000
r_work: 0.4888 rms_B_bonded: 16.61 restraints_weight: 8.0000
r_work (final): 0.4888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3100
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1563  Z= 0.118
  Angle     :  0.541   4.899   2108  Z= 0.270
  Chirality :  0.043   0.177    251
  Planarity :  0.004   0.033    269
  Dihedral  :  3.867  12.920    210
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.14 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.91 (0.60), residues: 195
  helix:  1.10 (0.50), residues: 109
  sheet:  0.31 (0.83), residues: 38
  loop : -0.02 (0.89), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG 3 175 
 TYR   0.003   0.002   TYR 3 284 
 PHE   0.009   0.002   PHE 3 268 
 HIS   0.001   0.000   HIS 3 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 1563)
  covalent geometry    : angle       0.54145 ( 2108)
  hydrogen bonds       : bond        0.02808 (   71)
  hydrogen bonds       : angle       4.68030 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.067 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 17
  average time/residue: 0.5113
  time to fit residues: 8.9057
Evaluate side-chains
  17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  324 ASN
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 3 optimal weight:    0.0870
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.5764

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

Flipped N/Q/H residues before XYZ refinement:
3 159 GLN
3 202 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.118619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.104123 restraints weight = 239638.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.4841 rms_B_bonded: 61.90
r_work: 0.4396 rms_B_bonded: 43.29 restraints_weight: 2.0000
r_work: 0.4511 rms_B_bonded: 32.86 restraints_weight: 4.0000
r_work: 0.4868 rms_B_bonded: 14.36 restraints_weight: 8.0000
r_work (final): 0.4868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3563
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   1563  Z= 0.119
  Angle     :  0.547   6.534   2108  Z= 0.265
  Chirality :  0.042   0.150    251
  Planarity :  0.004   0.026    269
  Dihedral  :  3.989  14.331    210
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.30 %
    Favored  : 88.95 %
  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:  0.84 (0.62), residues: 195
  helix:  1.08 (0.51), residues: 107
  sheet:  0.12 (0.90), residues: 38
  loop :  0.05 (0.91), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 3 175 
 TYR   0.001   0.000   TYR 3 284 
 PHE   0.007   0.001   PHE 3 268 
 HIS   0.000   0.000   HIS 3 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 1563)
  covalent geometry    : angle       0.54663 ( 2108)
  hydrogen bonds       : bond        0.02809 (   71)
  hydrogen bonds       : angle       4.84789 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.070 
Fit side-chains
REVERT: 3  146 LYS cc_start: 0.9543 (tppt) cc_final: 0.9305 (tppt)
REVERT: 3  191 PHE cc_start: -0.3060 (p90) cc_final: -0.3396 (p90)
REVERT: 3  221 MET cc_start: 0.1721 (mmt) cc_final: 0.0965 (tmm)
REVERT: 3  275 MET cc_start: 0.6830 (ptt) cc_final: 0.6081 (pmm)
  outliers start: 3
  outliers final: 1
  residues processed: 17
  average time/residue: 0.5551
  time to fit residues: 9.6645
Evaluate side-chains
  15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 15 optimal weight:   20.0000
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   overall best weight:    5.1190

-------------------------------------------------------------------------------
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 = 0.4967 r_free = 0.4967 target = 0.114745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.106573 restraints weight = 20991.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.4886 rms_B_bonded: 8.06
r_work (final): 0.4886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2639
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1563  Z= 0.148
  Angle     :  0.632   8.589   2108  Z= 0.310
  Chirality :  0.043   0.161    251
  Planarity :  0.005   0.044    269
  Dihedral  :  4.469  16.260    210
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.72 %
    Favored  : 88.95 %
  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:  0.40 (0.63), residues: 195
  helix:  0.88 (0.53), residues: 107
  sheet: -0.33 (1.00), residues: 28
  loop : -0.35 (0.86), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 3 292 
 TYR   0.008   0.004   TYR 3 284 
 PHE   0.013   0.002   PHE 3 294 
 HIS   0.002   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 1563)
  covalent geometry    : angle       0.63193 ( 2108)
  hydrogen bonds       : bond        0.03427 (   71)
  hydrogen bonds       : angle       5.41671 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.080 
Fit side-chains
REVERT: 3  221 MET cc_start: 0.1417 (mmt) cc_final: 0.1178 (tmm)
REVERT: 3  275 MET cc_start: 0.4920 (ptt) cc_final: 0.4315 (pmm)
  outliers start: 4
  outliers final: 1
  residues processed: 18
  average time/residue: 0.6347
  time to fit residues: 11.6245
Evaluate side-chains
  15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 14 optimal weight:   30.0000
   chunk 16 optimal weight:    7.9990
   chunk 3 optimal weight:   40.0000
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    5.7788

-------------------------------------------------------------------------------
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 = 0.4978 r_free = 0.4978 target = 0.112437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.107019 restraints weight = 27152.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.4970 rms_B_bonded: 7.76
r_work (final): 0.4970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2892
moved from start:          0.7067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   1563  Z= 0.182
  Angle     :  0.696  14.497   2108  Z= 0.332
  Chirality :  0.043   0.129    251
  Planarity :  0.005   0.032    269
  Dihedral  :  4.809  17.110    210
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.05 %
    Favored  : 87.21 %
  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: -0.02 (0.64), residues: 195
  helix:  0.74 (0.55), residues: 107
  sheet: -0.67 (1.07), residues: 28
  loop : -0.87 (0.79), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 3 292 
 TYR   0.006   0.003   TYR 3 284 
 PHE   0.013   0.002   PHE 3 230 
 HIS   0.002   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 1563)
  covalent geometry    : angle       0.69619 ( 2108)
  hydrogen bonds       : bond        0.04022 (   71)
  hydrogen bonds       : angle       5.74066 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.045 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 15
  average time/residue: 0.5162
  time to fit residues: 7.9259
Evaluate side-chains
  15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  191 PHE
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 11 optimal weight:   30.0000
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.4939 r_free = 0.4939 target = 0.116342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.108220 restraints weight = 21230.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4857 rms_B_bonded: 10.18
r_work (final): 0.4857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2722
moved from start:          0.7727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   1563  Z= 0.162
  Angle     :  0.747  15.449   2108  Z= 0.339
  Chirality :  0.042   0.134    251
  Planarity :  0.005   0.031    269
  Dihedral  :  4.792  16.915    210
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 23.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.37 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.26 (0.63), residues: 195
  helix:  0.59 (0.54), residues: 107
  sheet: -1.23 (0.92), residues: 39
  loop : -0.58 (0.79), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG 3 175 
 TYR   0.006   0.002   TYR 3 284 
 PHE   0.009   0.001   PHE 3 230 
 HIS   0.002   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 1563)
  covalent geometry    : angle       0.74722 ( 2108)
  hydrogen bonds       : bond        0.03984 (   71)
  hydrogen bonds       : angle       6.06765 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 3  221 MET cc_start: 0.5414 (tmm) cc_final: 0.5144 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 17
  average time/residue: 0.4900
  time to fit residues: 8.5350
Evaluate side-chains
  17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  191 PHE
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 13 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 6 optimal weight:   30.0000
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   overall best weight:    4.6988

-------------------------------------------------------------------------------
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 = 0.4847 r_free = 0.4847 target = 0.114091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.105248 restraints weight = 24542.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.4746 rms_B_bonded: 11.16
r_work (final): 0.4746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2412
moved from start:          0.8398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   1563  Z= 0.150
  Angle     :  0.737  14.956   2108  Z= 0.336
  Chirality :  0.042   0.123    251
  Planarity :  0.005   0.026    269
  Dihedral  :  4.751  15.631    210
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.53 %
    Favored  : 84.30 %
  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: -0.23 (0.63), residues: 195
  helix:  0.59 (0.54), residues: 105
  sheet: -1.67 (0.86), residues: 38
  loop : -0.08 (0.89), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG 3 154 
 TYR   0.005   0.002   TYR 3 284 
 PHE   0.009   0.001   PHE 3 230 
 HIS   0.002   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 1563)
  covalent geometry    : angle       0.73715 ( 2108)
  hydrogen bonds       : bond        0.03557 (   71)
  hydrogen bonds       : angle       6.04621 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.039 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 17
  average time/residue: 0.4576
  time to fit residues: 7.9480
Evaluate side-chains
  17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  328 ASP
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:   40.0000
   chunk 9 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.111274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.102421 restraints weight = 21799.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.4709 rms_B_bonded: 10.11
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2680
moved from start:          0.9214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   1563  Z= 0.184
  Angle     :  0.815  14.660   2108  Z= 0.382
  Chirality :  0.044   0.135    251
  Planarity :  0.005   0.030    269
  Dihedral  :  4.943  16.826    210
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 27.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.70 %
    Favored  : 81.98 %
  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: -0.03 (0.65), residues: 195
  helix:  0.65 (0.55), residues: 104
  sheet: -1.61 (0.90), residues: 37
  loop :  0.24 (0.91), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG 3 175 
 TYR   0.006   0.003   TYR 3 284 
 PHE   0.021   0.002   PHE 3 329 
 HIS   0.003   0.002   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 1563)
  covalent geometry    : angle       0.81493 ( 2108)
  hydrogen bonds       : bond        0.04394 (   71)
  hydrogen bonds       : angle       6.50447 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.039 
Fit side-chains
REVERT: 3  275 MET cc_start: 0.4193 (ptt) cc_final: 0.3722 (pmm)
  outliers start: 4
  outliers final: 1
  residues processed: 19
  average time/residue: 0.4341
  time to fit residues: 8.3884
Evaluate side-chains
  16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 6 optimal weight:   40.0000
   chunk 5 optimal weight:    0.3980
   chunk 14 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    5.2788

-------------------------------------------------------------------------------
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 = 0.4954 r_free = 0.4954 target = 0.111329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.101653 restraints weight = 21331.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4715 rms_B_bonded: 10.85
r_work (final): 0.4715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2770
moved from start:          0.9569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   1563  Z= 0.168
  Angle     :  0.847  15.678   2108  Z= 0.394
  Chirality :  0.046   0.161    251
  Planarity :  0.005   0.029    269
  Dihedral  :  4.930  16.546    210
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 17.44 %
    Favored  : 81.98 %
  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: -0.24 (0.64), residues: 195
  helix:  0.49 (0.53), residues: 104
  sheet: -1.62 (0.91), residues: 36
  loop :  0.03 (0.91), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG 3 175 
 TYR   0.010   0.003   TYR 3 284 
 PHE   0.023   0.002   PHE 3 230 
 HIS   0.002   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 1563)
  covalent geometry    : angle       0.84680 ( 2108)
  hydrogen bonds       : bond        0.03837 (   71)
  hydrogen bonds       : angle       6.47176 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.038 
Fit side-chains
REVERT: 3  275 MET cc_start: 0.4645 (ptt) cc_final: 0.4138 (pmm)
  outliers start: 1
  outliers final: 1
  residues processed: 16
  average time/residue: 0.3512
  time to fit residues: 5.7466
Evaluate side-chains
  16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    0.4980
   chunk 17 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:   40.0000
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:    6.2988

-------------------------------------------------------------------------------
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 = 0.4882 r_free = 0.4882 target = 0.108903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.099525 restraints weight = 19171.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.4685 rms_B_bonded: 9.75
r_work (final): 0.4685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3097
moved from start:          1.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   1563  Z= 0.201
  Angle     :  0.912  16.484   2108  Z= 0.423
  Chirality :  0.047   0.146    251
  Planarity :  0.006   0.034    269
  Dihedral  :  5.237  17.669    210
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 36.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 16.86 %
    Favored  : 81.98 %
  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: -0.63 (0.63), residues: 195
  helix:  0.22 (0.52), residues: 102
  sheet: -1.78 (0.93), residues: 35
  loop : -0.29 (0.88), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 3 175 
 TYR   0.013   0.004   TYR 3 284 
 PHE   0.023   0.002   PHE 3 230 
 HIS   0.003   0.002   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 1563)
  covalent geometry    : angle       0.91230 ( 2108)
  hydrogen bonds       : bond        0.04568 (   71)
  hydrogen bonds       : angle       6.87200 (  210)

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

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

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  390 Ramachandran restraints generated.
    195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.063 
Fit side-chains
REVERT: 3  275 MET cc_start: 0.5117 (ptt) cc_final: 0.4274 (pmm)
  outliers start: 2
  outliers final: 1
  residues processed: 15
  average time/residue: 0.4250
  time to fit residues: 6.5317
Evaluate side-chains
  14 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 3 residue  336 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 13 optimal weight:    0.0770
   chunk 8 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    4.3144

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

Flipped N/Q/H residues before XYZ refinement:
** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.110091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.098720 restraints weight = 15736.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4704 rms_B_bonded: 9.73
r_work (final): 0.4704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2740
moved from start:          1.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   1563  Z= 0.166
  Angle     :  0.898  16.330   2108  Z= 0.409
  Chirality :  0.045   0.143    251
  Planarity :  0.005   0.028    269
  Dihedral  :  5.062  15.094    210
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 28.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.44 %
    Favored  : 81.40 %
  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: -0.76 (0.62), residues: 195
  helix:  0.23 (0.53), residues: 102
  sheet: -1.89 (0.92), residues: 34
  loop : -0.62 (0.83), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG 3 154 
 TYR   0.009   0.003   TYR 3 284 
 PHE   0.018   0.002   PHE 3 230 
 HIS   0.001   0.001   HIS 3 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 1563)
  covalent geometry    : angle       0.89803 ( 2108)
  hydrogen bonds       : bond        0.03774 (   71)
  hydrogen bonds       : angle       6.61233 (  210)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1319.17 seconds
wall clock time: 23 minutes 23.25 seconds (1403.25 seconds total)