Starting phenix.real_space_refine
on Wed Sep 17 03:20:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j7v_61211/09_2025/9j7v_61211.map"
  }
  resolution = 3.3
  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=   0.001 sd=   0.038
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       3      5.49       5
     S      12      5.16       5
     C    2000      2.51       5
     N     449      2.21       5
     O     511      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: 2975
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2828
          Classifications: {'peptide': 352}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335}
    Chain: "A"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 147
          Unusual residues: {'POV': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 269
          Unresolved non-hydrogen angles: 318
          Unresolved non-hydrogen dihedrals: 243
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-1': 5}
          Unresolved non-hydrogen planarities: 33
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" C1  POV A 401 " occ=0.75
      ... (31 atoms not shown)
      pdb="C215 POV A 401 " occ=0.75
    residue:
      pdb=" C1  POV A 407 " occ=0.75
      ... (26 atoms not shown)
      pdb=" P   POV A 407 " occ=0.75
    residue:
      pdb=" C1  POV A 408 " occ=0.75
      ... (26 atoms not shown)
      pdb="C210 POV A 408 " occ=0.75
  Time building chain proxies: 0.98, per 1000 atoms: 0.33
  Number of scatterers: 2975
  At special positions: 0
  Unit cell: (68.85, 72.25, 75.65, 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      12     16.00
     P       3     15.00
     O     511      8.00
     N     449      7.00
     C    2000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 245 " distance=2.03

  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: 0.32
  Conformation dependent library (CDL) restraints added in 128.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      79.0% 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 'A' and resid 1 through 23
    Processing helix  chain 'A' and resid 26 through 37
    Processing helix  chain 'A' and resid 38 through 45
      removed outlier: 3.922A  pdb=" N   ALA A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.938A  pdb=" N   ILE A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 80
      removed outlier: 4.177A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
      removed outlier: 4.924A  pdb=" N   LEU A  89 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
      removed outlier: 4.561A  pdb=" N   ASN A  96 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'A' and resid 145 through 173
      removed outlier: 3.571A  pdb=" N   ARG A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 195
      removed outlier: 3.744A  pdb=" N   GLY A 184 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 230
    Processing helix  chain 'A' and resid 236 through 245
      removed outlier: 3.847A  pdb=" N   LYS A 240 " --> pdb=" O   TRP A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 277
    Processing helix  chain 'A' and resid 277 through 283
    Processing helix  chain 'A' and resid 291 through 310
      removed outlier: 3.525A  pdb=" N   ARG A 295 " --> pdb=" O   TRP A 291 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 331
    Processing helix  chain 'A' and resid 331 through 349
      removed outlier: 3.801A  pdb=" N   LEU A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ILE A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      Proline residue:  A 342  - end of helix

    194 hydrogen bonds defined for protein.
    579 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: 0.39

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 428
        1.31 -     1.44: 910
        1.44 -     1.56: 1701
        1.56 -     1.69: 3
        1.69 -     1.82: 17
  Bond restraints: 3059
  Sorted by residual:
  bond pdb=" O12 POV A 408 "
       pdb=" P   POV A 408 "
    ideal  model  delta    sigma   weight residual
    1.657  1.509  0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" O12 POV A 401 "
       pdb=" P   POV A 401 "
    ideal  model  delta    sigma   weight residual
    1.657  1.510  0.147 2.00e-02 2.50e+03 5.43e+01
  bond pdb=" O12 POV A 407 "
       pdb=" P   POV A 407 "
    ideal  model  delta    sigma   weight residual
    1.657  1.510  0.147 2.00e-02 2.50e+03 5.42e+01
  bond pdb=" C31 POV A 407 "
       pdb=" O31 POV A 407 "
    ideal  model  delta    sigma   weight residual
    1.327  1.400 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C31 POV A 401 "
       pdb=" O31 POV A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.399 -0.072 2.00e-02 2.50e+03 1.31e+01
  ... (remaining 3054 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 4054
        2.40 -     4.79: 45
        4.79 -     7.19: 19
        7.19 -     9.59: 17
        9.59 -    11.99: 7
  Bond angle restraints: 4142
  Sorted by residual:
  angle pdb=" O11 POV A 401 "
        pdb=" P   POV A 401 "
        pdb=" O12 POV A 401 "
      ideal   model   delta    sigma   weight residual
      97.67  109.66  -11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" O11 POV A 407 "
        pdb=" P   POV A 407 "
        pdb=" O12 POV A 407 "
      ideal   model   delta    sigma   weight residual
      97.67  109.62  -11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" O13 POV A 401 "
        pdb=" P   POV A 401 "
        pdb=" O14 POV A 401 "
      ideal   model   delta    sigma   weight residual
     121.11  109.21   11.90 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" O11 POV A 408 "
        pdb=" P   POV A 408 "
        pdb=" O12 POV A 408 "
      ideal   model   delta    sigma   weight residual
      97.67  109.39  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" O13 POV A 407 "
        pdb=" P   POV A 407 "
        pdb=" O14 POV A 407 "
      ideal   model   delta    sigma   weight residual
     121.11  109.42   11.69 3.00e+00 1.11e-01 1.52e+01
  ... (remaining 4137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.01: 1685
       31.01 -    62.03: 78
       62.03 -    93.04: 4
       93.04 -   124.05: 0
      124.05 -   155.07: 1
  Dihedral angle restraints: 1768
    sinusoidal: 741
      harmonic: 1027
  Sorted by residual:
  dihedral pdb=" CA  ILE A  78 "
           pdb=" C   ILE A  78 "
           pdb=" N   LEU A  79 "
           pdb=" CA  LEU A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.44  -22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" C3  POV A 407 "
           pdb=" C31 POV A 407 "
           pdb=" O31 POV A 407 "
           pdb=" C32 POV A 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
     172.61  -32.32 -155.07     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" CA  TYR A  85 "
           pdb=" C   TYR A  85 "
           pdb=" N   TRP A  86 "
           pdb=" CA  TRP A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.97   16.03     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 250
       0.025 -    0.051: 119
       0.051 -    0.076: 54
       0.076 -    0.102: 21
       0.102 -    0.127: 9
  Chirality restraints: 453
  Sorted by residual:
  chirality pdb=" CA  PHE A 195 "
            pdb=" N   PHE A 195 "
            pdb=" C   PHE A 195 "
            pdb=" CB  PHE A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  THR A 255 "
            pdb=" N   THR A 255 "
            pdb=" C   THR A 255 "
            pdb=" CB  THR A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  TYR A  85 "
            pdb=" N   TYR A  85 "
            pdb=" C   TYR A  85 "
            pdb=" CB  TYR A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.34e-01
  ... (remaining 450 not shown)

  Planarity restraints: 498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  86 "    0.024 2.00e-02 2.50e+03   1.87e-02 8.72e+00
        pdb=" CG  TRP A  86 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  86 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  86 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 105 "    0.019 5.00e-02 4.00e+02   2.93e-02 1.37e+00
        pdb=" N   PRO A 106 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 106 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 106 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 143 "   -0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO A 144 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 144 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 144 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 495 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 331
        2.75 -     3.29: 2682
        3.29 -     3.82: 4697
        3.82 -     4.36: 5010
        4.36 -     4.90: 9402
  Nonbonded interactions: 22122
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  69 "
            pdb=" ND2 ASN A 264 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG  SER A  34 "
            pdb=" NH1 ARG A 170 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   SER A 200 "
            pdb=" OG  SER A 200 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   PRO A 144 "
            pdb=" OG1 THR A 145 "
     model   vdw
     2.498 3.040
  nonbonded pdb=" OH  TYR A  85 "
            pdb=" O   GLU A 110 "
     model   vdw
     2.500 3.040
  ... (remaining 22117 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.75 max=1.00 mean=0.99
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:                  0.010
  Normalize map: mean=0, sd=1:             1.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.730
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
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      :  0.007   0.148   3060  Z= 0.367
  Angle     :  0.974  11.987   4144  Z= 0.373
  Chirality :  0.039   0.127    453
  Planarity :  0.004   0.029    498
  Dihedral  : 16.846 155.067   1105
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.49), residues: 350
  helix:  2.07 (0.34), residues: 271
  sheet:  None (None), residues: 0
  loop : -1.58 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.010   0.001   TYR A  85 
 PHE   0.010   0.001   PHE A 217 
 TRP   0.050   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00747 ( 3059)
  covalent geometry    : angle       0.97422 ( 4142)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       0.81221 (    2)
  hydrogen bonds       : bond        0.13401 (  194)
  hydrogen bonds       : angle       4.31646 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.7827 (m110) cc_final: 0.7527 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0732
  time to fit residues: 2.9759
Evaluate side-chains
  27 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.145207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117256 restraints weight = 3874.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.30
r_work: 0.2938 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.0637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3060  Z= 0.121
  Angle     :  0.487   5.994   4144  Z= 0.250
  Chirality :  0.039   0.121    453
  Planarity :  0.004   0.033    498
  Dihedral  : 13.890 120.746    481
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.15 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.48), residues: 350
  helix:  2.15 (0.34), residues: 268
  sheet:  None (None), residues: 0
  loop : -1.17 (0.69), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 281 
 TYR   0.009   0.001   TYR A 127 
 PHE   0.010   0.001   PHE A 217 
 TRP   0.035   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3059)
  covalent geometry    : angle       0.48704 ( 4142)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.57737 (    2)
  hydrogen bonds       : bond        0.04717 (  194)
  hydrogen bonds       : angle       3.72076 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.7419 (m110) cc_final: 0.7020 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0771
  time to fit residues: 2.7198
Evaluate side-chains
  29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.140241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.112440 restraints weight = 3813.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.23
r_work: 0.2932 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3060  Z= 0.127
  Angle     :  0.477   5.833   4144  Z= 0.245
  Chirality :  0.039   0.121    453
  Planarity :  0.004   0.034    498
  Dihedral  : 13.333 110.910    481
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.36 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.48), residues: 350
  helix:  2.08 (0.34), residues: 268
  sheet:  None (None), residues: 0
  loop : -1.17 (0.69), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 281 
 TYR   0.010   0.001   TYR A 127 
 PHE   0.009   0.001   PHE A 217 
 TRP   0.026   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3059)
  covalent geometry    : angle       0.47684 ( 4142)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.44200 (    2)
  hydrogen bonds       : bond        0.04686 (  194)
  hydrogen bonds       : angle       3.70830 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.7433 (m110) cc_final: 0.7035 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0755
  time to fit residues: 2.5838
Evaluate side-chains
  29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0020
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 13 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117389 restraints weight = 3780.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.23
r_work: 0.3213 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3060  Z= 0.104
  Angle     :  0.449   5.682   4144  Z= 0.230
  Chirality :  0.038   0.121    453
  Planarity :  0.004   0.033    498
  Dihedral  : 12.862 101.561    481
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.00 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.48), residues: 350
  helix:  2.20 (0.34), residues: 267
  sheet:  None (None), residues: 0
  loop : -1.25 (0.69), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.009   0.001   TYR A 127 
 PHE   0.009   0.001   PHE A 217 
 TRP   0.022   0.001   TRP A  86 
 HIS   0.002   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3059)
  covalent geometry    : angle       0.44943 ( 4142)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.44281 (    2)
  hydrogen bonds       : bond        0.04187 (  194)
  hydrogen bonds       : angle       3.63824 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8129 (mmm) cc_final: 0.7912 (mmp)
REVERT: A   22 ASN cc_start: 0.7790 (m110) cc_final: 0.7420 (m110)
  outliers start: 2
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0635
  time to fit residues: 2.2993
Evaluate side-chains
  28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   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 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.142018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.114531 restraints weight = 3766.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.22
r_work: 0.3190 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3060  Z= 0.115
  Angle     :  0.460   5.722   4144  Z= 0.233
  Chirality :  0.039   0.121    453
  Planarity :  0.003   0.033    498
  Dihedral  : 12.638  91.126    481
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 12.94 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.48), residues: 350
  helix:  2.03 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.24 (0.74), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.009   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.019   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3059)
  covalent geometry    : angle       0.46007 ( 4142)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.43980 (    2)
  hydrogen bonds       : bond        0.04290 (  194)
  hydrogen bonds       : angle       3.63224 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8107 (mmm) cc_final: 0.7885 (mmp)
REVERT: A   22 ASN cc_start: 0.7823 (m110) cc_final: 0.7447 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0684
  time to fit residues: 2.4206
Evaluate side-chains
  29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   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 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.145041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117240 restraints weight = 3850.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.29
r_work: 0.3207 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3060  Z= 0.116
  Angle     :  0.460   5.720   4144  Z= 0.233
  Chirality :  0.039   0.121    453
  Planarity :  0.003   0.033    498
  Dihedral  : 12.535  79.185    481
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 13.59 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.48), residues: 350
  helix:  2.04 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.21 (0.74), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.009   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.018   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3059)
  covalent geometry    : angle       0.45968 ( 4142)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.45321 (    2)
  hydrogen bonds       : bond        0.04279 (  194)
  hydrogen bonds       : angle       3.62567 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8127 (mmm) cc_final: 0.7901 (mmp)
REVERT: A   22 ASN cc_start: 0.7843 (m110) cc_final: 0.7467 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0652
  time to fit residues: 2.2994
Evaluate side-chains
  28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0050
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.142640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.115151 restraints weight = 3774.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.23
r_work: 0.3225 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3060  Z= 0.104
  Angle     :  0.449   5.661   4144  Z= 0.227
  Chirality :  0.038   0.120    453
  Planarity :  0.003   0.032    498
  Dihedral  : 12.298  64.957    481
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.27 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.48), residues: 350
  helix:  2.09 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.20 (0.75), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.009   0.001   TYR A  85 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.018   0.001   TRP A  86 
 HIS   0.002   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3059)
  covalent geometry    : angle       0.44860 ( 4142)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       0.44659 (    2)
  hydrogen bonds       : bond        0.04065 (  194)
  hydrogen bonds       : angle       3.59829 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8116 (mmm) cc_final: 0.7883 (mmp)
REVERT: A   22 ASN cc_start: 0.7836 (m110) cc_final: 0.7464 (m110)
  outliers start: 2
  outliers final: 2
  residues processed: 30
  average time/residue: 0.0625
  time to fit residues: 2.3878
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 15 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115737 restraints weight = 3887.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.25
r_work: 0.3201 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3060  Z= 0.131
  Angle     :  0.474   5.787   4144  Z= 0.240
  Chirality :  0.039   0.121    453
  Planarity :  0.003   0.032    498
  Dihedral  : 12.036  67.439    481
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.59 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.48), residues: 350
  helix:  1.98 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.21 (0.75), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.008   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.017   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3059)
  covalent geometry    : angle       0.47449 ( 4142)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       0.43933 (    2)
  hydrogen bonds       : bond        0.04462 (  194)
  hydrogen bonds       : angle       3.64800 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8147 (mmm) cc_final: 0.7914 (mmp)
REVERT: A   22 ASN cc_start: 0.7877 (m110) cc_final: 0.7620 (m110)
REVERT: A  281 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7973 (ttp80)
  outliers start: 2
  outliers final: 2
  residues processed: 30
  average time/residue: 0.0648
  time to fit residues: 2.4895
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 4 optimal weight:    0.0040
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114897 restraints weight = 3864.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.25
r_work: 0.3219 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3060  Z= 0.104
  Angle     :  0.451   5.673   4144  Z= 0.229
  Chirality :  0.038   0.120    453
  Planarity :  0.003   0.032    498
  Dihedral  : 11.667  69.634    481
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.27 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.49), residues: 350
  helix:  2.09 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.17 (0.75), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.009   0.001   TYR A  85 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.018   0.001   TRP A  86 
 HIS   0.002   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3059)
  covalent geometry    : angle       0.45130 ( 4142)
  SS BOND              : bond        0.00193 (    1)
  SS BOND              : angle       0.45770 (    2)
  hydrogen bonds       : bond        0.04097 (  194)
  hydrogen bonds       : angle       3.60234 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8121 (mmm) cc_final: 0.7882 (mmp)
REVERT: A   22 ASN cc_start: 0.7860 (m110) cc_final: 0.7458 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 31
  average time/residue: 0.0646
  time to fit residues: 2.5477
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.143927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116635 restraints weight = 3817.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.23
r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3060  Z= 0.117
  Angle     :  0.461   5.728   4144  Z= 0.234
  Chirality :  0.039   0.120    453
  Planarity :  0.003   0.031    498
  Dihedral  : 11.387  70.614    481
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.59 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.48), residues: 350
  helix:  2.04 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.21 (0.75), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.008   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.017   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3059)
  covalent geometry    : angle       0.46102 ( 4142)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.47003 (    2)
  hydrogen bonds       : bond        0.04229 (  194)
  hydrogen bonds       : angle       3.62147 (  579)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A    5 MET cc_start: 0.8118 (mmm) cc_final: 0.7879 (mmp)
REVERT: A   22 ASN cc_start: 0.7861 (m110) cc_final: 0.7455 (m110)
  outliers start: 2
  outliers final: 2
  residues processed: 30
  average time/residue: 0.0590
  time to fit residues: 2.2892
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.143602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.116293 restraints weight = 3815.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.22
r_work: 0.3212 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3060  Z= 0.124
  Angle     :  0.470   5.750   4144  Z= 0.238
  Chirality :  0.039   0.121    453
  Planarity :  0.003   0.031    498
  Dihedral  : 11.178  71.260    481
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.92 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.48), residues: 350
  helix:  1.99 (0.33), residues: 274
  sheet:  None (None), residues: 0
  loop : -1.23 (0.74), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.008   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.017   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3059)
  covalent geometry    : angle       0.46959 ( 4142)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.47186 (    2)
  hydrogen bonds       : bond        0.04374 (  194)
  hydrogen bonds       : angle       3.64039 (  579)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 855.98 seconds
wall clock time: 15 minutes 20.65 seconds (920.65 seconds total)