Starting phenix.real_space_refine
on Wed Sep 17 05:24:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c07_45075/09_2025/9c07_45075.map"
  }
  resolution = 2.73
  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=   0.003 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       4      8.98       5
     S      28      5.16       5
     C    3050      2.51       5
     N     708      2.21       5
     O     722      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4512
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "U"
      Number of atoms: 2108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2108
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 5, 'TRANS': 256}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2108
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 5, 'TRANS': 256}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 148
          Unusual residues: {'D12': 4, 'EIC': 1, 'HEX': 8, 'OCT': 4}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
    Chain: "A"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 148
          Unusual residues: {'  K': 4, 'D12': 2, 'EIC': 1, 'HEX': 6, 'OCT': 4, 'R16': 2}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
  Time building chain proxies: 1.40, per 1000 atoms: 0.31
  Number of scatterers: 4512
  At special positions: 0
  Unit cell: (67.635, 85.17, 98.53, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       4     19.00
     S      28     16.00
     O     722      8.00
     N     708      7.00
     C    3050      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: 0.52
  Conformation dependent library (CDL) restraints added in 158.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  972

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      78.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'U' and resid 14 through 65
      removed outlier: 5.455A  pdb=" N   ALA U  44 " --> pdb=" O   ALA U  40 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   HIS U  45 " --> pdb=" O   LEU U  41 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   HIS U  64 " --> pdb=" O   PHE U  60 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 67 through 83
    Processing helix  chain 'U' and resid 97 through 109
    Processing helix  chain 'U' and resid 124 through 166
      Proline residue:  U 136  - end of helix
      removed outlier: 3.710A  pdb=" N   ARG U 166 " --> pdb=" O   GLN U 162 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 193 through 215
      removed outlier: 3.781A  pdb=" N   MET U 215 " --> pdb=" O   CYS U 211 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 223 through 236
    Processing helix  chain 'U' and resid 255 through 295
      removed outlier: 3.706A  pdb=" N   PHE U 259 " --> pdb=" O   GLY U 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 64
      removed outlier: 5.451A  pdb=" N   ALA A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   HIS A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 85
    Processing helix  chain 'A' and resid 96 through 109
    Processing helix  chain 'A' and resid 124 through 166
      Proline residue:  A 136  - end of helix
      removed outlier: 3.689A  pdb=" N   ARG A 166 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 220
      removed outlier: 3.518A  pdb=" N   MET A 215 " --> pdb=" O   CYS A 211 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
    Processing helix  chain 'A' and resid 223 through 236
    Processing helix  chain 'A' and resid 255 through 294
      removed outlier: 3.798A  pdb=" N   PHE A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    1005 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: 0.64

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 757
        1.33 -     1.45: 1208
        1.45 -     1.57: 2577
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 4582
  Sorted by residual:
  bond pdb=" N   ILE U 219 "
       pdb=" CA  ILE U 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.23e-02 6.61e+03 6.71e+00
  bond pdb=" N   HIS U 250 "
       pdb=" CA  HIS U 250 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.28e-02 6.10e+03 4.82e+00
  bond pdb=" N   TRP U 289 "
       pdb=" CA  TRP U 289 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.79e+00
  bond pdb=" N   TYR U 251 "
       pdb=" CA  TYR U 251 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 1.44e-02 4.82e+03 4.53e+00
  bond pdb=" C1  EIC U 414 "
       pdb=" O2  EIC U 414 "
    ideal  model  delta    sigma   weight residual
    1.250  1.208  0.042 2.00e-02 2.50e+03 4.51e+00
  ... (remaining 4577 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 5924
        1.61 -     3.21: 122
        3.21 -     4.82: 23
        4.82 -     6.43: 4
        6.43 -     8.03: 3
  Bond angle restraints: 6076
  Sorted by residual:
  angle pdb=" CA  TYR U 216 "
        pdb=" CB  TYR U 216 "
        pdb=" CG  TYR U 216 "
      ideal   model   delta    sigma   weight residual
     113.90  121.00   -7.10 1.80e+00 3.09e-01 1.55e+01
  angle pdb=" N   TYR U 216 "
        pdb=" CA  TYR U 216 "
        pdb=" C   TYR U 216 "
      ideal   model   delta    sigma   weight residual
     113.28  107.13    6.15 1.57e+00 4.06e-01 1.53e+01
  angle pdb=" C   MET U 215 "
        pdb=" N   TYR U 216 "
        pdb=" CA  TYR U 216 "
      ideal   model   delta    sigma   weight residual
     126.45  119.68    6.77 1.77e+00 3.19e-01 1.46e+01
  angle pdb=" N   GLU A 252 "
        pdb=" CA  GLU A 252 "
        pdb=" C   GLU A 252 "
      ideal   model   delta    sigma   weight residual
     110.80  102.77    8.03 2.13e+00 2.20e-01 1.42e+01
  angle pdb=" N   ASN A 288 "
        pdb=" CA  ASN A 288 "
        pdb=" C   ASN A 288 "
      ideal   model   delta    sigma   weight residual
     111.07  107.44    3.63 1.07e+00 8.73e-01 1.15e+01
  ... (remaining 6071 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.96: 2340
       11.96 -    23.91: 216
       23.91 -    35.87: 67
       35.87 -    47.82: 36
       47.82 -    59.78: 21
  Dihedral angle restraints: 2680
    sinusoidal: 1162
      harmonic: 1518
  Sorted by residual:
  dihedral pdb=" CA  ASP U  96 "
           pdb=" C   ASP U  96 "
           pdb=" N   PHE U  97 "
           pdb=" CA  PHE U  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.68   26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  TRP A  95 "
           pdb=" C   TRP A  95 "
           pdb=" N   ASP A  96 "
           pdb=" CA  ASP A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.08   19.92     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  ASP A  89 "
           pdb=" C   ASP A  89 "
           pdb=" N   ASN A  90 "
           pdb=" CA  ASN A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 2677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 476
       0.033 -    0.066: 117
       0.066 -    0.099: 33
       0.099 -    0.132: 13
       0.132 -    0.164: 7
  Chirality restraints: 646
  Sorted by residual:
  chirality pdb=" CA  THR U 110 "
            pdb=" N   THR U 110 "
            pdb=" C   THR U 110 "
            pdb=" CB  THR U 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CA  ALA U 249 "
            pdb=" N   ALA U 249 "
            pdb=" C   ALA U 249 "
            pdb=" CB  ALA U 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.65   -0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CB  THR U 110 "
            pdb=" CA  THR U 110 "
            pdb=" OG1 THR U 110 "
            pdb=" CG2 THR U 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.40e-01
  ... (remaining 643 not shown)

  Planarity restraints: 732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG U  68 "    0.274 9.50e-02 1.11e+02   1.23e-01 9.24e+00
        pdb=" NE  ARG U  68 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG U  68 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG U  68 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG U  68 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR U 110 "   -0.009 2.00e-02 2.50e+03   1.94e-02 3.74e+00
        pdb=" C   THR U 110 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR U 110 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE U 111 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 110 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.29e+00
        pdb=" C   THR A 110 "    0.026 2.00e-02 2.50e+03
        pdb=" O   THR A 110 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 111 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 729 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.84: 1490
        2.84 -     3.42: 4985
        3.42 -     3.99: 7754
        3.99 -     4.57: 11582
        4.57 -     5.14: 16725
  Nonbonded interactions: 42536
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU U 220 "
            pdb=" OH  TYR U 257 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER U 109 "
            pdb=" OG1 THR U 110 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR U  78 "
            pdb=" OE2 GLU A  79 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   ASN A 277 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" NH1 ARG A  19 "
            pdb=" OD1 ASN A 288 "
     model   vdw
     2.392 3.120
  ... (remaining 42531 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 14 through 295 or resid 408 or resid 410 through 414))
  selection = (chain 'U' and (resid 14 through 295 or resid 408 or resid 410 through 414))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.590
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
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   0.042   4582  Z= 0.227
  Angle     :  0.583   8.031   6076  Z= 0.353
  Chirality :  0.038   0.164    646
  Planarity :  0.005   0.123    732
  Dihedral  : 12.727  59.778   1708
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.60 %
    Favored  : 96.17 %
  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:  4.88 (0.39), residues: 516
  helix:  4.11 (0.25), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.19 (0.64), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U  19 
 TYR   0.010   0.001   TYR A  30 
 PHE   0.011   0.001   PHE A 232 
 TRP   0.010   0.001   TRP A  53 
 HIS   0.002   0.001   HIS U  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4582)
  covalent geometry    : angle       0.58309 ( 6076)
  hydrogen bonds       : bond        0.10002 (  335)
  hydrogen bonds       : angle       3.54219 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: U   59 GLN cc_start: 0.8808 (tp40) cc_final: 0.8494 (tm-30)
REVERT: A  162 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8502 (tm130)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 1.0357
  time to fit residues: 68.6804
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3197 r_free = 0.3197 target = 0.087760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.068788 restraints weight = 8593.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.39
r_work: 0.2698 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4582  Z= 0.132
  Angle     :  0.511   5.626   6076  Z= 0.275
  Chirality :  0.034   0.148    646
  Planarity :  0.003   0.024    732
  Dihedral  : 11.893  58.824    772
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.56 %
    Favored  : 90.54 %
  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:  4.92 (0.38), residues: 516
  helix:  4.12 (0.24), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.05 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U 292 
 TYR   0.018   0.001   TYR A 155 
 PHE   0.008   0.001   PHE U 262 
 TRP   0.010   0.001   TRP U 289 
 HIS   0.003   0.001   HIS U  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4582)
  covalent geometry    : angle       0.51077 ( 6076)
  hydrogen bonds       : bond        0.05389 (  335)
  hydrogen bonds       : angle       2.88613 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.176 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7802 (mp10) cc_final: 0.7534 (mp10)
REVERT: U  155 TYR cc_start: 0.7938 (t80) cc_final: 0.7524 (m-80)
REVERT: A  155 TYR cc_start: 0.7989 (t80) cc_final: 0.7578 (t80)
REVERT: A  162 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8718 (tm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 41
  average time/residue: 0.8065
  time to fit residues: 34.0495
Evaluate side-chains
  39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0670
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3220 r_free = 0.3220 target = 0.089243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.070428 restraints weight = 8665.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.43
r_work: 0.2730 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4582  Z= 0.117
  Angle     :  0.458   4.853   6076  Z= 0.249
  Chirality :  0.033   0.134    646
  Planarity :  0.003   0.022    732
  Dihedral  : 10.508  59.614    772
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.01 %
    Favored  : 90.32 %
  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:  4.93 (0.38), residues: 516
  helix:  4.14 (0.24), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.13 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 166 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.008   0.001   PHE A 262 
 TRP   0.009   0.001   TRP U  95 
 HIS   0.004   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4582)
  covalent geometry    : angle       0.45813 ( 6076)
  hydrogen bonds       : bond        0.04942 (  335)
  hydrogen bonds       : angle       2.75889 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.169 
Fit side-chains
REVERT: U   48 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7662 (mm-40)
REVERT: U   65 GLN cc_start: 0.7722 (mp10) cc_final: 0.7326 (mp10)
REVERT: U  155 TYR cc_start: 0.7801 (t80) cc_final: 0.7471 (t80)
REVERT: A   65 GLN cc_start: 0.7680 (pm20) cc_final: 0.7445 (pm20)
REVERT: A  155 TYR cc_start: 0.7856 (t80) cc_final: 0.7414 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 43
  average time/residue: 0.8179
  time to fit residues: 36.2201
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   48 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.088929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.069928 restraints weight = 8484.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.42
r_work: 0.2729 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4582  Z= 0.119
  Angle     :  0.453   4.892   6076  Z= 0.247
  Chirality :  0.033   0.131    646
  Planarity :  0.002   0.021    732
  Dihedral  :  9.483  59.099    772
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.23 %
    Favored  : 90.09 %
  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:  4.91 (0.38), residues: 516
  helix:  4.18 (0.24), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.28 (0.64), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U 292 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.008   0.001   PHE A 262 
 TRP   0.008   0.001   TRP U  95 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4582)
  covalent geometry    : angle       0.45285 ( 6076)
  hydrogen bonds       : bond        0.04978 (  335)
  hydrogen bonds       : angle       2.73820 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.131 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7773 (mp10) cc_final: 0.7351 (mp10)
REVERT: U  155 TYR cc_start: 0.7904 (t80) cc_final: 0.7532 (t80)
REVERT: A  155 TYR cc_start: 0.7977 (t80) cc_final: 0.7579 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.8063
  time to fit residues: 34.0485
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   90 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3196 r_free = 0.3196 target = 0.087755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.068669 restraints weight = 8604.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.42
r_work: 0.2704 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4582  Z= 0.125
  Angle     :  0.459   4.939   6076  Z= 0.252
  Chirality :  0.033   0.132    646
  Planarity :  0.002   0.020    732
  Dihedral  :  8.926  59.698    772
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.81 %
    Favored  : 88.74 %
  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:  4.92 (0.38), residues: 516
  helix:  4.19 (0.24), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.26 (0.64), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U 292 
 TYR   0.009   0.001   TYR A 155 
 PHE   0.008   0.001   PHE A 262 
 TRP   0.007   0.001   TRP U  95 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4582)
  covalent geometry    : angle       0.45874 ( 6076)
  hydrogen bonds       : bond        0.05124 (  335)
  hydrogen bonds       : angle       2.75614 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.184 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7771 (mp10) cc_final: 0.7478 (mp10)
REVERT: U  155 TYR cc_start: 0.7832 (t80) cc_final: 0.7450 (t80)
REVERT: A  155 TYR cc_start: 0.7877 (t80) cc_final: 0.7446 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 0.8706
  time to fit residues: 36.7356
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   90 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.091522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.072539 restraints weight = 8644.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.45
r_work: 0.2781 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4582  Z= 0.105
  Angle     :  0.436   5.583   6076  Z= 0.237
  Chirality :  0.032   0.125    646
  Planarity :  0.002   0.020    732
  Dihedral  :  7.917  57.579    772
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 11.94 %
    Favored  : 87.84 %
  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:  5.03 (0.38), residues: 516
  helix:  4.20 (0.24), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.01 (0.65), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 292 
 TYR   0.008   0.001   TYR A  30 
 PHE   0.007   0.001   PHE U 232 
 TRP   0.010   0.001   TRP U  95 
 HIS   0.002   0.000   HIS U 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 4582)
  covalent geometry    : angle       0.43628 ( 6076)
  hydrogen bonds       : bond        0.04265 (  335)
  hydrogen bonds       : angle       2.59408 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.178 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7625 (mp10) cc_final: 0.7344 (mp10)
REVERT: U  155 TYR cc_start: 0.7825 (t80) cc_final: 0.7422 (t80)
REVERT: A  155 TYR cc_start: 0.7748 (t80) cc_final: 0.7277 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 41
  average time/residue: 0.7771
  time to fit residues: 32.8211
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3193 r_free = 0.3193 target = 0.087515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.068628 restraints weight = 8752.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 2.45
r_work: 0.2705 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2591 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4582  Z= 0.134
  Angle     :  0.493   7.577   6076  Z= 0.267
  Chirality :  0.033   0.133    646
  Planarity :  0.002   0.019    732
  Dihedral  :  8.342  56.997    772
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 12.61 %
    Favored  : 87.16 %
  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:  5.04 (0.38), residues: 516
  helix:  4.26 (0.24), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.17 (0.66), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U  83 
 TYR   0.008   0.001   TYR U  30 
 PHE   0.008   0.001   PHE A 262 
 TRP   0.007   0.001   TRP U  53 
 HIS   0.003   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4582)
  covalent geometry    : angle       0.49318 ( 6076)
  hydrogen bonds       : bond        0.05222 (  335)
  hydrogen bonds       : angle       2.76016 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.165 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7836 (mp10) cc_final: 0.7520 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 40
  average time/residue: 0.8185
  time to fit residues: 33.7413
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.087358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.068550 restraints weight = 8632.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.43
r_work: 0.2697 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4582  Z= 0.136
  Angle     :  0.503   7.305   6076  Z= 0.272
  Chirality :  0.033   0.132    646
  Planarity :  0.002   0.019    732
  Dihedral  :  8.357  57.289    772
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 1.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 12.84 %
    Favored  : 86.71 %
  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:  5.00 (0.38), residues: 516
  helix:  4.23 (0.24), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.19 (0.65), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U  83 
 TYR   0.007   0.001   TYR A  30 
 PHE   0.007   0.001   PHE A 262 
 TRP   0.007   0.001   TRP U  95 
 HIS   0.003   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4582)
  covalent geometry    : angle       0.50314 ( 6076)
  hydrogen bonds       : bond        0.05217 (  335)
  hydrogen bonds       : angle       2.75814 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.174 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7788 (mp10) cc_final: 0.7475 (mp10)
REVERT: U  155 TYR cc_start: 0.7679 (t80) cc_final: 0.7427 (t80)
REVERT: A  155 TYR cc_start: 0.7631 (t80) cc_final: 0.7380 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 39
  average time/residue: 0.8345
  time to fit residues: 33.5280
Evaluate side-chains
  39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0980
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0570
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.091053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.072019 restraints weight = 8499.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.44
r_work: 0.2781 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   4582  Z= 0.115
  Angle     :  0.484   6.971   6076  Z= 0.260
  Chirality :  0.032   0.126    646
  Planarity :  0.002   0.020    732
  Dihedral  :  7.617  54.792    772
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 12.84 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.09 (0.38), residues: 516
  helix:  4.29 (0.24), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.13 (0.66), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U 292 
 TYR   0.008   0.001   TYR A  30 
 PHE   0.007   0.001   PHE U 232 
 TRP   0.010   0.001   TRP U  95 
 HIS   0.002   0.000   HIS U 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4582)
  covalent geometry    : angle       0.48428 ( 6076)
  hydrogen bonds       : bond        0.04321 (  335)
  hydrogen bonds       : angle       2.59461 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.170 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7605 (mp10) cc_final: 0.7351 (mp10)
REVERT: U  155 TYR cc_start: 0.7584 (t80) cc_final: 0.7333 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 40
  average time/residue: 0.8355
  time to fit residues: 34.3697
Evaluate side-chains
  37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3207 r_free = 0.3207 target = 0.088562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.069586 restraints weight = 8582.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.44
r_work: 0.2740 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4582  Z= 0.129
  Angle     :  0.512   7.509   6076  Z= 0.277
  Chirality :  0.033   0.154    646
  Planarity :  0.002   0.018    732
  Dihedral  :  7.828  54.816    772
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  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:  5.12 (0.38), residues: 516
  helix:  4.26 (0.24), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.96 (0.67), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 292 
 TYR   0.008   0.001   TYR A  30 
 PHE   0.007   0.001   PHE A 262 
 TRP   0.007   0.001   TRP U  95 
 HIS   0.002   0.000   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4582)
  covalent geometry    : angle       0.51243 ( 6076)
  hydrogen bonds       : bond        0.04867 (  335)
  hydrogen bonds       : angle       2.68279 ( 1005)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.172 
Fit side-chains
REVERT: U   65 GLN cc_start: 0.7700 (mp10) cc_final: 0.7438 (mp10)
REVERT: U  155 TYR cc_start: 0.7583 (t80) cc_final: 0.7342 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.8439
  time to fit residues: 33.0360
Evaluate side-chains
  37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.089208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.070248 restraints weight = 8574.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.44
r_work: 0.2746 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4582  Z= 0.123
  Angle     :  0.505   8.150   6076  Z= 0.273
  Chirality :  0.033   0.141    646
  Planarity :  0.002   0.019    732
  Dihedral  :  7.643  54.828    772
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  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:  5.11 (0.38), residues: 516
  helix:  4.25 (0.24), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.95 (0.67), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 292 
 TYR   0.007   0.001   TYR A  30 
 PHE   0.007   0.001   PHE A 262 
 TRP   0.008   0.001   TRP U  95 
 HIS   0.002   0.000   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4582)
  covalent geometry    : angle       0.50495 ( 6076)
  hydrogen bonds       : bond        0.04677 (  335)
  hydrogen bonds       : angle       2.64843 ( 1005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1561.44 seconds
wall clock time: 27 minutes 27.80 seconds (1647.80 seconds total)