Starting phenix.real_space_refine
on Fri Aug 22 12:39:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2025/8ggy_40025.cif"
  }
  resolution = 3.9
  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=   0.018
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      13      5.16       5
     C    1388      2.51       5
     N     339      2.21       5
     O     356      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: 2096
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2081
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.02, per 1000 atoms: 0.49
  Number of scatterers: 2096
  At special positions: 0
  Unit cell: (54.6651, 85.9023, 62.4744, 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      13     16.00
     O     356      8.00
     N     339      7.00
     C    1388      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: 0.31
  Conformation dependent library (CDL) restraints added in 131.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      85.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.619A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 86
    Processing helix  chain 'R' and resid 86 through 96
    Processing helix  chain 'R' and resid 103 through 137
      removed outlier: 4.335A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG R 131 " --> pdb=" O   ILE R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.690A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.760A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.719A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.788A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.774A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 316
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 3.584A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.513A  pdb=" N   LEU R 340 " --> pdb=" O   PHE R 336 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    480 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: 0.31

  Time building geometry restraints manager: 0.39 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: 643
        1.34 -     1.46: 589
        1.46 -     1.58: 900
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 2151
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.453 -0.056 2.00e-02 2.50e+03 7.78e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.578 -0.055 2.00e-02 2.50e+03 7.56e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.443 -0.049 2.00e-02 2.50e+03 6.08e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.51e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.497 -0.046 2.00e-02 2.50e+03 5.21e+00
  ... (remaining 2146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 2843
        1.38 -     2.75: 77
        2.75 -     4.13: 19
        4.13 -     5.51: 10
        5.51 -     6.88: 2
  Bond angle restraints: 2951
  Sorted by residual:
  angle pdb=" C   GLU R 180 "
        pdb=" N   ALA R 181 "
        pdb=" CA  ALA R 181 "
      ideal   model   delta    sigma   weight residual
     121.54  128.17   -6.63 1.91e+00 2.74e-01 1.21e+01
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     120.72  116.07    4.65 1.67e+00 3.59e-01 7.75e+00
  angle pdb=" CB  MET R 279 "
        pdb=" CG  MET R 279 "
        pdb=" SD  MET R 279 "
      ideal   model   delta    sigma   weight residual
     112.70  119.58   -6.88 3.00e+00 1.11e-01 5.26e+00
  angle pdb=" CA  GLN R 337 "
        pdb=" CB  GLN R 337 "
        pdb=" CG  GLN R 337 "
      ideal   model   delta    sigma   weight residual
     114.10  118.62   -4.52 2.00e+00 2.50e-01 5.10e+00
  angle pdb=" C   ASP R 300 "
        pdb=" N   ASN R 301 "
        pdb=" CA  ASN R 301 "
      ideal   model   delta    sigma   weight residual
     123.05  126.33   -3.28 1.57e+00 4.06e-01 4.36e+00
  ... (remaining 2946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 1088
       15.70 -    31.39: 95
       31.39 -    47.09: 32
       47.09 -    62.78: 5
       62.78 -    78.48: 4
  Dihedral angle restraints: 1224
    sinusoidal: 396
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.67  -15.33     0      5.00e+00 4.00e-02 9.40e+00
  dihedral pdb=" CA  ARG R 131 "
           pdb=" CB  ARG R 131 "
           pdb=" CG  ARG R 131 "
           pdb=" CD  ARG R 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.96  -53.04     3      1.50e+01 4.44e-03 9.17e+00
  dihedral pdb=" CA  ILE R 325 "
           pdb=" C   ILE R 325 "
           pdb=" N   TYR R 326 "
           pdb=" CA  TYR R 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.11  -14.89     0      5.00e+00 4.00e-02 8.87e+00
  ... (remaining 1221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 237
       0.035 -    0.069: 91
       0.069 -    0.103: 22
       0.103 -    0.138: 3
       0.138 -    0.172: 1
  Chirality restraints: 354
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CA  ILE R 303 "
            pdb=" N   ILE R 303 "
            pdb=" C   ILE R 303 "
            pdb=" CB  ILE R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CB  VAL R 295 "
            pdb=" CA  VAL R 295 "
            pdb=" CG1 VAL R 295 "
            pdb=" CG2 VAL R 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 351 not shown)

  Planarity restraints: 363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO R 330 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 198 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   ALA R 198 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ALA R 198 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   TYR R 199 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.004 2.00e-02 2.50e+03   8.53e-03 7.27e-01
        pdb=" C   THR R 281 "    0.015 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 360 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 784
        2.88 -     3.39: 2232
        3.39 -     3.89: 3300
        3.89 -     4.40: 3172
        4.40 -     4.90: 5820
  Nonbonded interactions: 15308
  Sorted by model distance:
  nonbonded pdb=" O   ALA R  92 "
            pdb=" OG1 THR R  96 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" O   TRP R  99 "
            pdb=" OG1 THR R 100 "
     model   vdw
     2.438 3.040
  nonbonded pdb=" OD1 ASP R 130 "
            pdb=" N   ARG R 131 "
     model   vdw
     2.481 3.120
  nonbonded pdb=" O   GLN R 337 "
            pdb=" OE1 GLN R 337 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" O   ILE R 127 "
            pdb=" OD1 ASP R 130 "
     model   vdw
     2.585 3.040
  ... (remaining 15303 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.410
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.620
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
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      :  0.004   0.056   2151  Z= 0.195
  Angle     :  0.631   6.883   2951  Z= 0.330
  Chirality :  0.040   0.172    354
  Planarity :  0.004   0.044    363
  Dihedral  : 14.743  78.477    686
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 (0.51), residues: 277
  helix:  2.21 (0.36), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.51 (0.67), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.006   0.001   TYR R 326 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.013   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 2151)
  covalent geometry    : angle       0.63075 ( 2951)
  hydrogen bonds       : bond        0.13394 (  160)
  hydrogen bonds       : angle       4.58551 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0537
  time to fit residues: 2.9242
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.127399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.114236 restraints weight = 3804.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116988 restraints weight = 2043.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118952 restraints weight = 1259.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120311 restraints weight = 864.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.121205 restraints weight = 643.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2151  Z= 0.147
  Angle     :  0.570   5.733   2951  Z= 0.305
  Chirality :  0.040   0.132    354
  Planarity :  0.004   0.042    363
  Dihedral  :  3.981  15.414    312
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 11.92 %
    Favored  : 84.46 %
  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 (0.51), residues: 277
  helix:  2.02 (0.35), residues: 223
  sheet:  None (None), residues: 0
  loop : -1.31 (0.69), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 228 
 TYR   0.017   0.001   TYR R 308 
 PHE   0.016   0.001   PHE R 104 
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2151)
  covalent geometry    : angle       0.56979 ( 2951)
  hydrogen bonds       : bond        0.05657 (  160)
  hydrogen bonds       : angle       3.72343 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.079 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8491 (mm) cc_final: 0.8257 (mm)
  outliers start: 7
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0570
  time to fit residues: 2.8118
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0020
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0870
   overall best weight:    0.3366

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.134345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.121218 restraints weight = 3741.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.123954 restraints weight = 1996.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125996 restraints weight = 1236.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.127387 restraints weight = 845.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.128394 restraints weight = 627.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2151  Z= 0.120
  Angle     :  0.535   5.297   2951  Z= 0.285
  Chirality :  0.039   0.130    354
  Planarity :  0.004   0.040    363
  Dihedral  :  3.867  15.346    312
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 16.06 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.51), residues: 277
  helix:  2.03 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.21 (0.72), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 228 
 TYR   0.011   0.001   TYR R 308 
 PHE   0.018   0.001   PHE R 104 
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2151)
  covalent geometry    : angle       0.53492 ( 2951)
  hydrogen bonds       : bond        0.05022 (  160)
  hydrogen bonds       : angle       3.57626 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.080 
Fit side-chains
REVERT: R  318 ASN cc_start: 0.8534 (t0) cc_final: 0.8310 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 38
  average time/residue: 0.0602
  time to fit residues: 2.7390
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0000
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.127707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114746 restraints weight = 3737.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.117357 restraints weight = 2038.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.119281 restraints weight = 1282.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120616 restraints weight = 888.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.121613 restraints weight = 669.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2151  Z= 0.138
  Angle     :  0.555   5.985   2951  Z= 0.297
  Chirality :  0.040   0.128    354
  Planarity :  0.004   0.040    363
  Dihedral  :  3.924  15.331    312
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.58 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.51), residues: 277
  helix:  2.05 (0.35), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.31 (0.70), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.013   0.001   TYR R 308 
 PHE   0.018   0.001   PHE R 104 
 TRP   0.007   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2151)
  covalent geometry    : angle       0.55499 ( 2951)
  hydrogen bonds       : bond        0.05373 (  160)
  hydrogen bonds       : angle       3.60963 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0629
  time to fit residues: 2.4739
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 13 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 27 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** R 318 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 = 0.3462 r_free = 0.3462 target = 0.128536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115618 restraints weight = 3751.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118263 restraints weight = 2042.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120183 restraints weight = 1280.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121594 restraints weight = 885.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122513 restraints weight = 656.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2151  Z= 0.126
  Angle     :  0.546   5.427   2951  Z= 0.291
  Chirality :  0.039   0.132    354
  Planarity :  0.004   0.039    363
  Dihedral  :  3.858  15.403    312
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.13 %
    Favored  : 77.72 %
  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:  2.28 (0.51), residues: 277
  helix:  2.14 (0.35), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.39 (0.72), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.012   0.001   TYR R 308 
 PHE   0.017   0.001   PHE R 104 
 TRP   0.008   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2151)
  covalent geometry    : angle       0.54587 ( 2951)
  hydrogen bonds       : bond        0.05102 (  160)
  hydrogen bonds       : angle       3.57352 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.077 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0647
  time to fit residues: 2.5384
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.114429 restraints weight = 3715.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.117040 restraints weight = 2041.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.118955 restraints weight = 1281.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120146 restraints weight = 884.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.121048 restraints weight = 669.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2151  Z= 0.147
  Angle     :  0.570   5.738   2951  Z= 0.306
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.040    363
  Dihedral  :  3.987  15.608    312
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 18.65 %
    Favored  : 74.61 %
  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 (0.50), residues: 277
  helix:  2.06 (0.35), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.43 (0.72), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.014   0.001   TYR R 308 
 PHE   0.014   0.001   PHE R 104 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.001   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2151)
  covalent geometry    : angle       0.57042 ( 2951)
  hydrogen bonds       : bond        0.05754 (  160)
  hydrogen bonds       : angle       3.70577 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.088 
Fit side-chains
  outliers start: 13
  outliers final: 8
  residues processed: 39
  average time/residue: 0.0557
  time to fit residues: 2.6051
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112516 restraints weight = 3870.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.115248 restraints weight = 2103.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117192 restraints weight = 1308.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118420 restraints weight = 896.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119382 restraints weight = 667.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2151  Z= 0.143
  Angle     :  0.571   6.106   2951  Z= 0.305
  Chirality :  0.040   0.131    354
  Planarity :  0.004   0.040    363
  Dihedral  :  3.989  15.474    312
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 18.65 %
    Favored  : 75.65 %
  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:  2.19 (0.50), residues: 277
  helix:  2.05 (0.35), residues: 225
  sheet:  None (None), residues: 0
  loop : -1.28 (0.71), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.013   0.001   TYR R 308 
 PHE   0.014   0.001   PHE R 104 
 TRP   0.007   0.001   TRP R 109 
 HIS   0.001   0.000   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 2151)
  covalent geometry    : angle       0.57144 ( 2951)
  hydrogen bonds       : bond        0.05649 (  160)
  hydrogen bonds       : angle       3.69971 (  480)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.077 
Fit side-chains
REVERT: R  339 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8197 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 35
  average time/residue: 0.0541
  time to fit residues: 2.2909
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  279 MET
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  329 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2995 > 50:
  distance: 1 - 15:   4.148
  distance: 5 - 23:  13.869
  distance: 9 - 28:  30.781
  distance: 13 - 33:  18.142
  distance: 15 - 16:   3.446
  distance: 16 - 17:   5.638
  distance: 17 - 18:   8.070
  distance: 18 - 41:   9.534
  distance: 20 - 21:   6.739
  distance: 21 - 22:   4.261
  distance: 23 - 24:   5.309
  distance: 24 - 25:  12.899
  distance: 25 - 26:  24.025
  distance: 25 - 28:  20.365
  distance: 26 - 48:  14.427
  distance: 28 - 29:  39.639
  distance: 29 - 30:  11.150
  distance: 29 - 32:  25.820
  distance: 30 - 31:   4.814
  distance: 30 - 33:  10.179
  distance: 31 - 53:  14.942
  distance: 33 - 34:  10.467
  distance: 34 - 35:   4.029
  distance: 34 - 37:   8.304
  distance: 35 - 36:   6.685
  distance: 35 - 41:   4.197
  distance: 36 - 58:   4.708
  distance: 37 - 38:   8.180
  distance: 37 - 39:   4.293
  distance: 38 - 40:  13.364
  distance: 41 - 42:   4.970
  distance: 42 - 43:   3.417
  distance: 42 - 45:   4.746
  distance: 45 - 46:   3.249
  distance: 45 - 47:  10.800
  distance: 48 - 49:   5.939
  distance: 49 - 52:  10.165
  distance: 50 - 51:   3.532
  distance: 50 - 53:   3.641
  distance: 51 - 70:   4.009
  distance: 53 - 54:   4.680
  distance: 54 - 55:   4.304
  distance: 54 - 57:   8.349
  distance: 56 - 81:   7.270
  distance: 58 - 59:   3.139
  distance: 59 - 62:   3.568
  distance: 60 - 61:   3.745
  distance: 60 - 63:   5.302
  distance: 61 - 85:   5.161
  distance: 63 - 64:   4.689
  distance: 64 - 65:   4.056
  distance: 65 - 66:   3.758
  distance: 65 - 70:   3.305
  distance: 66 - 92:   5.506
  distance: 67 - 68:  11.258
  distance: 67 - 69:  10.367
  distance: 70 - 71:   3.766
  distance: 71 - 72:   6.949
  distance: 71 - 74:   3.180
  distance: 72 - 73:   7.875
  distance: 72 - 81:   4.336
  distance: 73 - 98:  13.306
  distance: 74 - 75:   7.049
  distance: 75 - 76:   5.527
  distance: 75 - 77:   8.194
  distance: 76 - 78:   8.626
  distance: 77 - 79:   6.593
  distance: 78 - 80:  11.294
  distance: 79 - 80:   8.607
  distance: 84 - 105:   3.004