Starting phenix.real_space_refine
on Fri Aug 22 15:24:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2025/8bf8_16016.cif"
  }
  resolution = 2.8
  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=   1.000
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
     P     111      5.49       5
     S       1      5.16       5
     C    2525      2.51       5
     N     871      2.21       5
     O    1178      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4686
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2303
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 7, 'TRANS': 294}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 212
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 112
    Chain: "B"
      Number of atoms: 2383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 2383
          Classifications: {'RNA': 111}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 16, 'rna3p': 94}
          Chain breaks: 2
  Time building chain proxies: 1.21, per 1000 atoms: 0.26
  Number of scatterers: 4686
  At special positions: 0
  Unit cell: (84.032, 87.36, 84.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       1     16.00
     P     111     15.00
     O    1178      8.00
     N     871      7.00
     C    2525      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: 0.35
  Conformation dependent library (CDL) restraints added in 68.4 milliseconds
  
  Enol-peptide restraints added in 0.0 nanoseconds
  

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  566

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 2 sheets defined
      53.6% alpha, 16.2% beta
      42 base pairs and 59 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 43
      removed outlier: 3.645A  pdb=" N   ILE A  21 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR A  43 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 65
    Processing helix  chain 'A' and resid 68 through 73
    Processing helix  chain 'A' and resid 75 through 94
      removed outlier: 3.766A  pdb=" N   LEU A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 232
    Processing helix  chain 'A' and resid 236 through 272
    Processing helix  chain 'A' and resid 299 through 315
    Processing helix  chain 'A' and resid 360 through 377
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121
      removed outlier: 4.057A  pdb=" N   LYS A 153 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   VAL A 157 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU A 168 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ARG A 161 " --> pdb=" O   HIS A 166 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   HIS A 166 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   TYR A 167 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A  10 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS A 143 " --> pdb=" O   TYR A  12 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201

    153 hydrogen bonds defined for protein.
    441 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      103 hydrogen bonds
      162 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      59 stacking parallelities
  Total time for adding SS restraints: 0.75

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 872
        1.33 -     1.45: 1746
        1.45 -     1.57: 2169
        1.57 -     1.68: 219
        1.68 -     1.80: 1
  Bond restraints: 5007
  Sorted by residual:
  bond pdb=" O3'   C B -63 "
       pdb=" P     C B -62 "
    ideal  model  delta    sigma   weight residual
    1.607  1.587  0.020 1.50e-02 4.44e+03 1.82e+00
  bond pdb=" C   GLY A 189 "
       pdb=" O   GLY A 189 "
    ideal  model  delta    sigma   weight residual
    1.243  1.233  0.010 9.30e-03 1.16e+04 1.15e+00
  bond pdb=" CB  TRP A 313 "
       pdb=" CG  TRP A 313 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.25e-01
  bond pdb=" CA  ILE A 177 "
       pdb=" CB  ILE A 177 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.014 1.55e-02 4.16e+03 8.01e-01
  bond pdb=" CB  PRO A 178 "
       pdb=" CG  PRO A 178 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.39e-01
  ... (remaining 5002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 7116
        1.20 -     2.40: 153
        2.40 -     3.60: 34
        3.60 -     4.80: 7
        4.80 -     5.99: 2
  Bond angle restraints: 7312
  Sorted by residual:
  angle pdb=" CA  TYR A 309 "
        pdb=" CB  TYR A 309 "
        pdb=" CG  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     113.90  119.89   -5.99 1.80e+00 3.09e-01 1.11e+01
  angle pdb=" O4'   A B -88 "
        pdb=" C1'   A B -88 "
        pdb=" N9    A B -88 "
      ideal   model   delta    sigma   weight residual
     108.20  112.12   -3.92 1.50e+00 4.44e-01 6.83e+00
  angle pdb=" C2'   G B -78 "
        pdb=" C1'   G B -78 "
        pdb=" N9    G B -78 "
      ideal   model   delta    sigma   weight residual
     112.00  114.91   -2.91 1.50e+00 4.44e-01 3.75e+00
  angle pdb=" C   THR A 123 "
        pdb=" N   ASN A 124 "
        pdb=" CA  ASN A 124 "
      ideal   model   delta    sigma   weight residual
     122.46  124.93   -2.47 1.41e+00 5.03e-01 3.07e+00
  angle pdb=" C2'   A B -88 "
        pdb=" C1'   A B -88 "
        pdb=" N9    A B -88 "
      ideal   model   delta    sigma   weight residual
     114.00  116.60   -2.60 1.50e+00 4.44e-01 3.00e+00
  ... (remaining 7307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2593
       17.34 -    34.68: 225
       34.68 -    52.02: 138
       52.02 -    69.36: 155
       69.36 -    86.70: 29
  Dihedral angle restraints: 3140
    sinusoidal: 2265
      harmonic: 875
  Sorted by residual:
  dihedral pdb=" O4'   U B -89 "
           pdb=" C1'   U B -89 "
           pdb=" N1    U B -89 "
           pdb=" C2    U B -89 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -84.08  -75.92     1      1.50e+01 4.44e-03 3.23e+01
  dihedral pdb=" CB  LYS A 233 "
           pdb=" CG  LYS A 233 "
           pdb=" CD  LYS A 233 "
           pdb=" CE  LYS A 233 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.41  -57.41     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" O5'   C B -67 "
           pdb=" C5'   C B -67 "
           pdb=" C4'   C B -67 "
           pdb=" C3'   C B -67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00   -1.26   56.26     3      1.50e+01 4.44e-03 9.39e+00
  ... (remaining 3137 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 796
       0.043 -    0.086: 89
       0.086 -    0.129: 26
       0.129 -    0.171: 0
       0.171 -    0.214: 1
  Chirality restraints: 912
  Sorted by residual:
  chirality pdb=" C1'   A B -88 "
            pdb=" O4'   A B -88 "
            pdb=" C2'   A B -88 "
            pdb=" N9    A B -88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.22    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  TYR A 309 "
            pdb=" N   TYR A 309 "
            pdb=" C   TYR A 309 "
            pdb=" CB  TYR A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  ILE A 275 "
            pdb=" N   ILE A 275 "
            pdb=" C   ILE A 275 "
            pdb=" CB  ILE A 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 909 not shown)

  Planarity restraints: 514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B -88 "   -0.028 2.00e-02 2.50e+03   1.38e-02 5.27e+00
        pdb=" N9    A B -88 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A B -88 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B -88 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A B -88 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A B -88 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B -88 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B -88 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A B -88 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A B -88 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A B -88 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B -78 "    0.026 2.00e-02 2.50e+03   1.08e-02 3.47e+00
        pdb=" N9    G B -78 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    G B -78 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G B -78 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B -78 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B -78 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G B -78 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    G B -78 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B -78 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G B -78 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G B -78 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B -78 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 309 "   -0.015 2.00e-02 2.50e+03   1.18e-02 2.76e+00
        pdb=" CG  TYR A 309 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 309 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 309 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 309 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 309 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 309 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 309 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 511 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 516
        2.74 -     3.28: 4367
        3.28 -     3.82: 9269
        3.82 -     4.36: 10882
        4.36 -     4.90: 15807
  Nonbonded interactions: 40841
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 261 "
            pdb=" OG1 THR A 265 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH2 ARG A 238 "
            pdb=" O6    G B -33 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O2'   A B -66 "
            pdb=" O2    C B -63 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O2    C B-107 "
            pdb=" N2    G B  -6 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   LYS A 263 "
            pdb=" OG  SER A 267 "
     model   vdw
     2.307 3.040
  ... (remaining 40836 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.970
  Find NCS groups from input model:        0.010
  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:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
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      :  0.003   0.043   5007  Z= 0.140
  Angle     :  0.474   5.995   7312  Z= 0.248
  Chirality :  0.031   0.214    912
  Planarity :  0.003   0.022    514
  Dihedral  : 21.432  86.703   2574
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  6.98 %
    Favored  : 92.09 %
  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:  0.92 (0.51), residues: 292
  helix:  2.03 (0.40), residues: 151
  sheet: -1.01 (0.85), residues: 44
  loop : -0.84 (0.67), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  29 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.009   0.001   PHE A  35 
 TRP   0.005   0.001   TRP A 313 
 HIS   0.005   0.002   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5007)
  covalent geometry    : angle       0.47404 ( 7312)
  hydrogen bonds       : bond        0.13139 (  256)
  hydrogen bonds       : angle       6.17931 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  168 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: A  214 TYR cc_start: 0.8208 (m-80) cc_final: 0.7977 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 35
  average time/residue: 0.6620
  time to fit residues: 23.9714
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0470
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.0882

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  64 GLN
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 ASN
A 147 GLN
A 156 ASN
A 227 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.204664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160159 restraints weight = 5122.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.37
r_work: 0.3738 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5007  Z= 0.201
  Angle     :  0.546   6.474   7312  Z= 0.281
  Chirality :  0.035   0.200    912
  Planarity :  0.004   0.021    514
  Dihedral  : 22.253  86.321   2071
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.49 %
    Favored  : 84.65 %
  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:  0.80 (0.50), residues: 292
  helix:  1.98 (0.40), residues: 152
  sheet: -2.42 (1.39), residues: 16
  loop : -0.92 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 110 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.014   0.002   PHE A  35 
 TRP   0.006   0.002   TRP A  70 
 HIS   0.004   0.002   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 5007)
  covalent geometry    : angle       0.54554 ( 7312)
  hydrogen bonds       : bond        0.05611 (  256)
  hydrogen bonds       : angle       4.30229 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6886 (tm130)
REVERT: A  168 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7700 (mt-10)
REVERT: A  174 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6476 (mt-10)
REVERT: A  214 TYR cc_start: 0.8233 (m-80) cc_final: 0.7898 (m-80)
REVERT: A  223 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6168 (mmp-170)
  outliers start: 4
  outliers final: 2
  residues processed: 30
  average time/residue: 0.5422
  time to fit residues: 17.0117
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** 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 = 0.4307 r_free = 0.4307 target = 0.208264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.164535 restraints weight = 5175.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 1.34
r_work: 0.3780 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5007  Z= 0.133
  Angle     :  0.490   6.031   7312  Z= 0.254
  Chirality :  0.032   0.210    912
  Planarity :  0.003   0.021    514
  Dihedral  : 22.142  83.653   2070
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.42 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.50), residues: 292
  helix:  2.24 (0.40), residues: 152
  sheet: -1.47 (1.04), residues: 24
  loop : -1.22 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.023   0.001   TYR A 309 
 PHE   0.013   0.001   PHE A  35 
 TRP   0.006   0.001   TRP A  70 
 HIS   0.004   0.002   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5007)
  covalent geometry    : angle       0.49006 ( 7312)
  hydrogen bonds       : bond        0.04860 (  256)
  hydrogen bonds       : angle       3.85222 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  168 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7540 (mt-10)
REVERT: A  223 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6113 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7327 (p90)
  outliers start: 5
  outliers final: 0
  residues processed: 30
  average time/residue: 0.6140
  time to fit residues: 19.1949
Evaluate side-chains
  24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.207170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.162973 restraints weight = 5149.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 1.34
r_work: 0.3759 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5007  Z= 0.158
  Angle     :  0.510   6.486   7312  Z= 0.263
  Chirality :  0.033   0.200    912
  Planarity :  0.003   0.021    514
  Dihedral  : 22.087  83.475   2070
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.81 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.49), residues: 292
  helix:  2.19 (0.39), residues: 152
  sheet: -1.46 (1.03), residues: 24
  loop : -1.32 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.011   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 300 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5007)
  covalent geometry    : angle       0.51024 ( 7312)
  hydrogen bonds       : bond        0.05067 (  256)
  hydrogen bonds       : angle       3.81735 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6767 (tm130)
REVERT: A  168 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: A  223 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6113 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7440 (p90)
  outliers start: 8
  outliers final: 3
  residues processed: 28
  average time/residue: 0.5617
  time to fit residues: 16.3898
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.203794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.158979 restraints weight = 5165.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 1.38
r_work: 0.3718 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5007  Z= 0.225
  Angle     :  0.562   6.956   7312  Z= 0.289
  Chirality :  0.035   0.193    912
  Planarity :  0.004   0.024    514
  Dihedral  : 22.120  83.834   2070
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.28 %
    Favored  : 80.00 %
  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:  0.59 (0.49), residues: 292
  helix:  1.94 (0.39), residues: 152
  sheet: -1.40 (1.07), residues: 24
  loop : -1.36 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  29 
 TYR   0.032   0.002   TYR A 309 
 PHE   0.010   0.002   PHE A  35 
 TRP   0.005   0.001   TRP A 313 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 5007)
  covalent geometry    : angle       0.56160 ( 7312)
  hydrogen bonds       : bond        0.05708 (  256)
  hydrogen bonds       : angle       3.96279 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.6774 (tm130)
REVERT: A  168 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7647 (mt-10)
REVERT: A  223 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6230 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7569 (p90)
  outliers start: 8
  outliers final: 2
  residues processed: 27
  average time/residue: 0.6641
  time to fit residues: 18.6296
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.205637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161095 restraints weight = 5224.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.34
r_work: 0.3740 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5007  Z= 0.174
  Angle     :  0.526   6.582   7312  Z= 0.271
  Chirality :  0.033   0.200    912
  Planarity :  0.003   0.020    514
  Dihedral  : 22.105  83.014   2070
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.21 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.49), residues: 292
  helix:  2.06 (0.39), residues: 152
  sheet: -1.55 (1.03), residues: 24
  loop : -1.34 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 313 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5007)
  covalent geometry    : angle       0.52553 ( 7312)
  hydrogen bonds       : bond        0.05298 (  256)
  hydrogen bonds       : angle       3.86821 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  147 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6807 (tm130)
REVERT: A  168 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7649 (mt-10)
REVERT: A  223 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6138 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7449 (p90)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.5941
  time to fit residues: 17.3121
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.208068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.163940 restraints weight = 5106.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 1.34
r_work: 0.3773 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5007  Z= 0.142
  Angle     :  0.512   7.169   7312  Z= 0.264
  Chirality :  0.032   0.206    912
  Planarity :  0.003   0.020    514
  Dihedral  : 22.035  81.705   2070
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.67 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.49), residues: 292
  helix:  2.28 (0.39), residues: 152
  sheet: -1.70 (1.01), residues: 24
  loop : -1.30 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.026   0.001   TYR A 309 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 300 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5007)
  covalent geometry    : angle       0.51246 ( 7312)
  hydrogen bonds       : bond        0.04918 (  256)
  hydrogen bonds       : angle       3.75684 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  110 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5690 (mtt180)
REVERT: A  147 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.6727 (tm130)
REVERT: A  168 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: A  223 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6114 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7287 (p90)
  outliers start: 7
  outliers final: 2
  residues processed: 28
  average time/residue: 0.7192
  time to fit residues: 20.8181
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0370
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.208929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.164811 restraints weight = 5243.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.36
r_work: 0.3782 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5007  Z= 0.139
  Angle     :  0.507   6.212   7312  Z= 0.261
  Chirality :  0.032   0.205    912
  Planarity :  0.003   0.021    514
  Dihedral  : 21.982  80.833   2070
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 16.74 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.49), residues: 292
  helix:  2.37 (0.39), residues: 152
  sheet: -0.99 (1.38), residues: 12
  loop : -1.52 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.027   0.001   TYR A 309 
 PHE   0.011   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 300 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5007)
  covalent geometry    : angle       0.50656 ( 7312)
  hydrogen bonds       : bond        0.04845 (  256)
  hydrogen bonds       : angle       3.73649 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  110 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5654 (mtt180)
REVERT: A  147 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6795 (tm130)
REVERT: A  168 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7561 (mt-10)
REVERT: A  174 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6295 (mm-30)
REVERT: A  213 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7968 (mtmm)
REVERT: A  223 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6182 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7320 (p90)
  outliers start: 9
  outliers final: 4
  residues processed: 29
  average time/residue: 0.6852
  time to fit residues: 20.6227
Evaluate side-chains
  30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 8 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.205558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161059 restraints weight = 5099.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.36
r_work: 0.3734 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5007  Z= 0.202
  Angle     :  0.548   6.746   7312  Z= 0.283
  Chirality :  0.034   0.194    912
  Planarity :  0.004   0.021    514
  Dihedral  : 21.997  81.131   2070
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.21 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.49), residues: 292
  helix:  2.16 (0.39), residues: 152
  sheet: -1.28 (1.32), residues: 12
  loop : -1.57 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.031   0.002   TYR A 309 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.005   0.001   TRP A 313 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5007)
  covalent geometry    : angle       0.54849 ( 7312)
  hydrogen bonds       : bond        0.05444 (  256)
  hydrogen bonds       : angle       3.87532 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  110 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5772 (mtt180)
REVERT: A  147 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (tp-100)
REVERT: A  168 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7687 (mt-10)
REVERT: A  174 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6442 (mm-30)
REVERT: A  223 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6157 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7545 (p90)
  outliers start: 8
  outliers final: 2
  residues processed: 31
  average time/residue: 0.6447
  time to fit residues: 20.7438
Evaluate side-chains
  32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 4 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.206489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.162077 restraints weight = 5205.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.35
r_work: 0.3750 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5007  Z= 0.173
  Angle     :  0.528   6.475   7312  Z= 0.275
  Chirality :  0.033   0.200    912
  Planarity :  0.004   0.020    514
  Dihedral  : 21.987  80.412   2070
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.21 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.48), residues: 292
  helix:  2.23 (0.39), residues: 152
  sheet: -1.00 (1.40), residues: 12
  loop : -1.57 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 300 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5007)
  covalent geometry    : angle       0.52839 ( 7312)
  hydrogen bonds       : bond        0.05200 (  256)
  hydrogen bonds       : angle       3.81358 (  603)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  110 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5783 (mtt180)
REVERT: A  147 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6766 (tm130)
REVERT: A  168 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: A  174 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6490 (mm-30)
REVERT: A  223 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6111 (mmp-170)
REVERT: A  309 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7447 (p90)
  outliers start: 7
  outliers final: 2
  residues processed: 29
  average time/residue: 0.6932
  time to fit residues: 20.8453
Evaluate side-chains
  31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0970
   chunk 5 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.206179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.161620 restraints weight = 5149.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 1.34
r_work: 0.3748 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5007  Z= 0.181
  Angle     :  0.532   6.515   7312  Z= 0.276
  Chirality :  0.033   0.199    912
  Planarity :  0.003   0.020    514
  Dihedral  : 21.977  79.985   2070
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.21 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.48), residues: 292
  helix:  2.20 (0.39), residues: 152
  sheet: -1.10 (1.36), residues: 12
  loop : -1.64 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.029   0.002   TYR A 309 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A 313 
 HIS   0.004   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5007)
  covalent geometry    : angle       0.53239 ( 7312)
  hydrogen bonds       : bond        0.05266 (  256)
  hydrogen bonds       : angle       3.82970 (  603)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1854.85 seconds
wall clock time: 32 minutes 23.10 seconds (1943.10 seconds total)