Starting phenix.real_space_refine
on Fri Aug 22 13:38:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ufe_42205/08_2025/8ufe_42205.map"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.144
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       1      5.49       5
     S      14      5.16       5
     C    2260      2.51       5
     N     571      2.21       5
     O     603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 3449
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3405
          Classifications: {'peptide': 470}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 450}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'PTY': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
  Time building chain proxies: 1.11, per 1000 atoms: 0.32
  Number of scatterers: 3449
  At special positions: 0
  Unit cell: (79.2, 64.9, 66, 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      14     16.00
     P       1     15.00
     O     603      8.00
     N     571      7.00
     C    2260      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: 0.20
  Conformation dependent library (CDL) restraints added in 84.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  826

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      84.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 38
      removed outlier: 4.488A  pdb=" N   SER A  31 " --> pdb=" O   TRP A  27 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ALA A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 61
      removed outlier: 3.884A  pdb=" N   LEU A  42 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   SER A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      Proline residue:  A  55  - end of helix
    Processing helix  chain 'A' and resid 64 through 81
      removed outlier: 3.865A  pdb=" N   TYR A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
    Processing helix  chain 'A' and resid 95 through 115
    Processing helix  chain 'A' and resid 118 through 147
      Proline residue:  A 138  - end of helix
      removed outlier: 3.720A  pdb=" N   LEU A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 179
    Processing helix  chain 'A' and resid 183 through 190
      removed outlier: 3.683A  pdb=" N   ALA A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 205
      removed outlier: 3.771A  pdb=" N   ILE A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 242
      removed outlier: 3.734A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 245 through 267
      removed outlier: 3.764A  pdb=" N   LEU A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 281 through 312
    Processing helix  chain 'A' and resid 316 through 342
      removed outlier: 4.288A  pdb=" N   VAL A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 346 through 366
    Processing helix  chain 'A' and resid 378 through 401
      Proline residue:  A 395  - end of helix
      removed outlier: 3.956A  pdb=" N   ILE A 401 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 443
      removed outlier: 4.119A  pdb=" N   GLY A 424 " --> pdb=" O   GLN A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
      removed outlier: 4.168A  pdb=" N   VAL A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 455
      No H-bonds generated for 'chain 'A' and resid 453 through 455'
    Processing helix  chain 'A' and resid 456 through 484
      removed outlier: 3.969A  pdb=" N   PHE A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    846 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: 0.40

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 534
        1.30 -     1.43: 838
        1.43 -     1.56: 2103
        1.56 -     1.69: 11
        1.69 -     1.82: 26
  Bond restraints: 3512
  Sorted by residual:
  bond pdb=" C30 PTY A 501 "
       pdb=" O4  PTY A 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.433 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C8  PTY A 501 "
       pdb=" O7  PTY A 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.432 -0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" C30 PTY A 501 "
       pdb=" C31 PTY A 501 "
    ideal  model  delta    sigma   weight residual
    1.504  1.554 -0.050 2.00e-02 2.50e+03 6.14e+00
  bond pdb=" C31 PTY A 501 "
       pdb=" C32 PTY A 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 2.00e-02 2.50e+03 4.47e+00
  bond pdb=" C11 PTY A 501 "
       pdb=" C8  PTY A 501 "
    ideal  model  delta    sigma   weight residual
    1.504  1.545 -0.041 2.00e-02 2.50e+03 4.22e+00
  ... (remaining 3507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 4732
        3.39 -     6.78: 48
        6.78 -    10.17: 4
       10.17 -    13.57: 3
       13.57 -    16.96: 1
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" O11 PTY A 501 "
        pdb=" P1  PTY A 501 "
        pdb=" O14 PTY A 501 "
      ideal   model   delta    sigma   weight residual
      92.90  109.86  -16.96 3.00e+00 1.11e-01 3.19e+01
  angle pdb=" N   ILE A  93 "
        pdb=" CA  ILE A  93 "
        pdb=" C   ILE A  93 "
      ideal   model   delta    sigma   weight residual
     111.81  108.56    3.25 8.60e-01 1.35e+00 1.43e+01
  angle pdb=" O12 PTY A 501 "
        pdb=" P1  PTY A 501 "
        pdb=" O13 PTY A 501 "
      ideal   model   delta    sigma   weight residual
     119.61  109.08   10.53 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" CA  LEU A 201 "
        pdb=" CB  LEU A 201 "
        pdb=" CG  LEU A 201 "
      ideal   model   delta    sigma   weight residual
     116.30  128.10  -11.80 3.50e+00 8.16e-02 1.14e+01
  angle pdb=" CB  MET A 104 "
        pdb=" CG  MET A 104 "
        pdb=" SD  MET A 104 "
      ideal   model   delta    sigma   weight residual
     112.70  121.80   -9.10 3.00e+00 1.11e-01 9.20e+00
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.84: 1807
       22.84 -    45.67: 190
       45.67 -    68.51: 37
       68.51 -    91.34: 8
       91.34 -   114.18: 1
  Dihedral angle restraints: 2043
    sinusoidal: 739
      harmonic: 1304
  Sorted by residual:
  dihedral pdb=" N1  PTY A 501 "
           pdb=" C2  PTY A 501 "
           pdb=" C3  PTY A 501 "
           pdb=" O11 PTY A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  179.51 -114.18     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" CA  ALA A 493 "
           pdb=" C   ALA A 493 "
           pdb=" N   HIS A 494 "
           pdb=" CA  HIS A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.14  -15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" C3  PTY A 501 "
           pdb=" O11 PTY A 501 "
           pdb=" P1  PTY A 501 "
           pdb=" O12 PTY A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.77   25.32  -85.09     1      3.00e+01 1.11e-03 9.75e+00
  ... (remaining 2040 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 377
       0.031 -    0.063: 153
       0.063 -    0.094: 47
       0.094 -    0.125: 16
       0.125 -    0.156: 2
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CB  ILE A  34 "
            pdb=" CA  ILE A  34 "
            pdb=" CG1 ILE A  34 "
            pdb=" CG2 ILE A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CA  SER A 137 "
            pdb=" N   SER A 137 "
            pdb=" C   SER A 137 "
            pdb=" CB  SER A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  PRO A 395 "
            pdb=" N   PRO A 395 "
            pdb=" C   PRO A 395 "
            pdb=" CB  PRO A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.14e-01
  ... (remaining 592 not shown)

  Planarity restraints: 592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 410 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 411 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 411 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 411 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 345 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO A 346 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  30 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" C   LEU A  30 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LEU A  30 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   SER A  31 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 589 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 402
        2.74 -     3.28: 3645
        3.28 -     3.82: 5862
        3.82 -     4.36: 6214
        4.36 -     4.90: 10917
  Nonbonded interactions: 27040
  Sorted by model distance:
  nonbonded pdb=" O   SER A  69 "
            pdb=" OG1 THR A  73 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OD2 ASP A  46 "
            pdb=" NE2 GLN A 129 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   GLY A  94 "
            pdb=" OG1 THR A  98 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER A  62 "
            pdb=" OG  SER A  62 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   GLY A 151 "
            pdb=" ND2 ASN A 155 "
     model   vdw
     2.378 3.120
  ... (remaining 27035 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.360
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
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      :  0.005   0.102   3512  Z= 0.240
  Angle     :  0.793  16.956   4788  Z= 0.357
  Chirality :  0.039   0.156    595
  Planarity :  0.004   0.034    592
  Dihedral  : 19.160 114.175   1217
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 40.59 %
    Favored  : 57.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.92 (0.40), residues: 468
  helix:  1.86 (0.27), residues: 348
  sheet:  None (None), residues: 0
  loop : -0.42 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 370 
 TYR   0.015   0.001   TYR A 200 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.004   0.000   TRP A 184 
 HIS   0.000   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 3512)
  covalent geometry    : angle       0.79324 ( 4788)
  hydrogen bonds       : bond        0.08277 (  284)
  hydrogen bonds       : angle       4.34539 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  104 MET cc_start: 0.8194 (mmm) cc_final: 0.7644 (mmt)
  outliers start: 6
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0368
  time to fit residues: 4.0387
Evaluate side-chains
  82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  310 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0030
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.189376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.170635 restraints weight = 5588.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.174650 restraints weight = 3187.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.177242 restraints weight = 2085.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.179226 restraints weight = 1515.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.180345 restraints weight = 1172.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.0485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3512  Z= 0.130
  Angle     :  0.572  11.094   4788  Z= 0.282
  Chirality :  0.038   0.141    595
  Planarity :  0.004   0.047    592
  Dihedral  : 11.743 124.761    545
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.70 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 38.53 %
    Favored  : 56.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.97 (0.39), residues: 468
  helix:  1.81 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.28 (0.67), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 370 
 TYR   0.005   0.001   TYR A  75 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.003   0.000   TRP A 470 
 HIS   0.000   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3512)
  covalent geometry    : angle       0.57245 ( 4788)
  hydrogen bonds       : bond        0.03923 (  284)
  hydrogen bonds       : angle       4.05355 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  104 MET cc_start: 0.8411 (mmm) cc_final: 0.8046 (mmt)
REVERT: A  143 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7344 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0351
  time to fit residues: 4.3067
Evaluate side-chains
  86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 34 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.195055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.177463 restraints weight = 5377.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.181573 restraints weight = 2884.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.184386 restraints weight = 1797.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.186223 restraints weight = 1237.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.187638 restraints weight = 930.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.0806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3512  Z= 0.137
  Angle     :  0.589  12.272   4788  Z= 0.288
  Chirality :  0.038   0.140    595
  Planarity :  0.004   0.048    592
  Dihedral  : 10.877 104.455    537
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 36.47 %
    Favored  : 57.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.39), residues: 468
  helix:  1.85 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.28 (0.67), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 370 
 TYR   0.005   0.001   TYR A 466 
 PHE   0.011   0.001   PHE A 327 
 TRP   0.003   0.000   TRP A 470 
 HIS   0.001   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3512)
  covalent geometry    : angle       0.58892 ( 4788)
  hydrogen bonds       : bond        0.03790 (  284)
  hydrogen bonds       : angle       4.01221 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   75 TYR cc_start: 0.8967 (t80) cc_final: 0.8741 (t80)
REVERT: A  104 MET cc_start: 0.8503 (mmm) cc_final: 0.8204 (mmt)
  outliers start: 19
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0340
  time to fit residues: 4.4589
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  441 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.179994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161280 restraints weight = 5097.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.165374 restraints weight = 2845.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.168244 restraints weight = 1828.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.170117 restraints weight = 1290.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.171499 restraints weight = 997.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3512  Z= 0.129
  Angle     :  0.584  12.291   4788  Z= 0.286
  Chirality :  0.039   0.142    595
  Planarity :  0.004   0.048    592
  Dihedral  : 10.516  89.301    537
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 36.18 %
    Favored  : 58.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.97 (0.39), residues: 468
  helix:  1.83 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.37 (0.66), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  88 
 TYR   0.005   0.001   TYR A 466 
 PHE   0.011   0.001   PHE A 327 
 TRP   0.004   0.000   TRP A 470 
 HIS   0.000   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3512)
  covalent geometry    : angle       0.58443 ( 4788)
  hydrogen bonds       : bond        0.03717 (  284)
  hydrogen bonds       : angle       3.94854 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   58 GLN cc_start: 0.7965 (tt0) cc_final: 0.7740 (tt0)
REVERT: A   75 TYR cc_start: 0.9073 (t80) cc_final: 0.8825 (t80)
REVERT: A  104 MET cc_start: 0.8336 (mmm) cc_final: 0.8063 (mmt)
  outliers start: 19
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0275
  time to fit residues: 3.6333
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  441 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.176875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.157416 restraints weight = 5288.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.161662 restraints weight = 2879.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.164652 restraints weight = 1843.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.166596 restraints weight = 1296.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.168211 restraints weight = 1000.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3512  Z= 0.159
  Angle     :  0.599  11.491   4788  Z= 0.297
  Chirality :  0.039   0.136    595
  Planarity :  0.004   0.049    592
  Dihedral  : 10.286  77.675    536
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 36.18 %
    Favored  : 57.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.81 (0.39), residues: 468
  helix:  1.70 (0.26), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.49 (0.67), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 370 
 TYR   0.006   0.001   TYR A 464 
 PHE   0.011   0.001   PHE A 161 
 TRP   0.003   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3512)
  covalent geometry    : angle       0.59946 ( 4788)
  hydrogen bonds       : bond        0.03843 (  284)
  hydrogen bonds       : angle       4.03845 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   75 TYR cc_start: 0.9018 (t80) cc_final: 0.8771 (t80)
REVERT: A  104 MET cc_start: 0.8390 (mmm) cc_final: 0.8107 (mmt)
REVERT: A  370 ARG cc_start: 0.7434 (ttt-90) cc_final: 0.7170 (ttt-90)
  outliers start: 22
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0360
  time to fit residues: 4.7788
Evaluate side-chains
  100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  441 PHE
Chi-restraints excluded: chain A residue  477 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.178316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.159349 restraints weight = 5200.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.163510 restraints weight = 2865.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.166324 restraints weight = 1835.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.168346 restraints weight = 1300.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.169445 restraints weight = 997.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3512  Z= 0.136
  Angle     :  0.604  12.662   4788  Z= 0.296
  Chirality :  0.039   0.137    595
  Planarity :  0.004   0.048    592
  Dihedral  : 10.114  77.004    536
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 36.76 %
    Favored  : 56.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.84 (0.39), residues: 468
  helix:  1.73 (0.27), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.44 (0.67), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 370 
 TYR   0.005   0.001   TYR A 466 
 PHE   0.009   0.001   PHE A 327 
 TRP   0.004   0.000   TRP A 470 
 HIS   0.000   0.000   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3512)
  covalent geometry    : angle       0.60412 ( 4788)
  hydrogen bonds       : bond        0.03675 (  284)
  hydrogen bonds       : angle       3.98230 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   75 TYR cc_start: 0.9078 (t80) cc_final: 0.8822 (t80)
REVERT: A  104 MET cc_start: 0.8352 (mmm) cc_final: 0.8134 (mmt)
REVERT: A  256 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7078 (mm)
REVERT: A  370 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.7075 (ttt-90)
  outliers start: 22
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0319
  time to fit residues: 4.5274
Evaluate side-chains
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  441 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0000
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.158797 restraints weight = 5326.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.163051 restraints weight = 2841.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.166038 restraints weight = 1786.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.168091 restraints weight = 1244.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.169570 restraints weight = 946.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3512  Z= 0.128
  Angle     :  0.626  11.626   4788  Z= 0.299
  Chirality :  0.039   0.136    595
  Planarity :  0.004   0.047    592
  Dihedral  :  9.935  76.757    536
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 38.24 %
    Favored  : 55.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.91 (0.39), residues: 468
  helix:  1.76 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.37 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 370 
 TYR   0.005   0.001   TYR A 464 
 PHE   0.008   0.001   PHE A 327 
 TRP   0.004   0.000   TRP A 470 
 HIS   0.000   0.000   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3512)
  covalent geometry    : angle       0.62574 ( 4788)
  hydrogen bonds       : bond        0.03613 (  284)
  hydrogen bonds       : angle       3.92236 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A   58 GLN cc_start: 0.8083 (tt0) cc_final: 0.7871 (tt0)
REVERT: A   75 TYR cc_start: 0.9014 (t80) cc_final: 0.8748 (t80)
REVERT: A  104 MET cc_start: 0.8325 (mmm) cc_final: 0.8092 (mmt)
REVERT: A  256 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7050 (mm)
REVERT: A  370 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.7136 (ttt-90)
  outliers start: 21
  outliers final: 16
  residues processed: 103
  average time/residue: 0.0347
  time to fit residues: 4.9058
Evaluate side-chains
  102 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  369 HIS
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0970
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.181098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.162274 restraints weight = 5256.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.166581 restraints weight = 2784.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.169564 restraints weight = 1720.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.171641 restraints weight = 1184.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.172980 restraints weight = 888.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3512  Z= 0.133
  Angle     :  0.647  13.877   4788  Z= 0.309
  Chirality :  0.040   0.149    595
  Planarity :  0.004   0.046    592
  Dihedral  :  9.840  76.824    536
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 38.53 %
    Favored  : 55.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.85 (0.39), residues: 468
  helix:  1.71 (0.27), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.39 (0.67), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 370 
 TYR   0.005   0.001   TYR A 464 
 PHE   0.008   0.001   PHE A 327 
 TRP   0.005   0.000   TRP A 470 
 HIS   0.000   0.000   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3512)
  covalent geometry    : angle       0.64721 ( 4788)
  hydrogen bonds       : bond        0.03624 (  284)
  hydrogen bonds       : angle       3.94364 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.9012 (t80) cc_final: 0.8763 (t80)
REVERT: A  256 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6991 (mm)
  outliers start: 22
  outliers final: 16
  residues processed: 104
  average time/residue: 0.0364
  time to fit residues: 5.1349
Evaluate side-chains
  102 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.180055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.161413 restraints weight = 5134.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.165713 restraints weight = 2749.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.168642 restraints weight = 1706.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.170574 restraints weight = 1179.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.172123 restraints weight = 895.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3512  Z= 0.141
  Angle     :  0.658  12.958   4788  Z= 0.315
  Chirality :  0.041   0.183    595
  Planarity :  0.004   0.046    592
  Dihedral  :  9.625  76.031    536
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.91 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 39.71 %
    Favored  : 54.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.73 (0.39), residues: 468
  helix:  1.64 (0.27), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.47 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 370 
 TYR   0.008   0.001   TYR A 464 
 PHE   0.008   0.001   PHE A 292 
 TRP   0.004   0.001   TRP A 470 
 HIS   0.000   0.000   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3512)
  covalent geometry    : angle       0.65777 ( 4788)
  hydrogen bonds       : bond        0.03706 (  284)
  hydrogen bonds       : angle       3.94732 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   58 GLN cc_start: 0.8021 (tt0) cc_final: 0.7807 (tt0)
REVERT: A   75 TYR cc_start: 0.9013 (t80) cc_final: 0.8753 (t80)
REVERT: A  256 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6988 (mm)
  outliers start: 19
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0273
  time to fit residues: 3.7307
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.181505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.162587 restraints weight = 5150.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.166938 restraints weight = 2706.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.169856 restraints weight = 1673.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.171768 restraints weight = 1157.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.173277 restraints weight = 880.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3512  Z= 0.155
  Angle     :  0.671  12.451   4788  Z= 0.326
  Chirality :  0.041   0.202    595
  Planarity :  0.004   0.047    592
  Dihedral  :  9.606  77.208    536
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.91 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 40.88 %
    Favored  : 53.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.58 (0.39), residues: 468
  helix:  1.52 (0.27), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.46 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 370 
 TYR   0.008   0.001   TYR A 464 
 PHE   0.009   0.001   PHE A 292 
 TRP   0.003   0.001   TRP A 184 
 HIS   0.000   0.000   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3512)
  covalent geometry    : angle       0.67140 ( 4788)
  hydrogen bonds       : bond        0.03811 (  284)
  hydrogen bonds       : angle       4.03705 (  846)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A   75 TYR cc_start: 0.8980 (t80) cc_final: 0.8726 (t80)
REVERT: A  256 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7132 (mm)
  outliers start: 19
  outliers final: 18
  residues processed: 105
  average time/residue: 0.0353
  time to fit residues: 5.1076
Evaluate side-chains
  105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 19 optimal weight:    0.0870
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.185180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.165895 restraints weight = 5131.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.170285 restraints weight = 2684.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.173306 restraints weight = 1658.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.175270 restraints weight = 1146.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176869 restraints weight = 873.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3512  Z= 0.137
  Angle     :  0.664  13.600   4788  Z= 0.321
  Chirality :  0.040   0.202    595
  Planarity :  0.004   0.045    592
  Dihedral  :  9.462  77.552    536
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.70 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 40.00 %
    Favored  : 53.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.63 (0.39), residues: 468
  helix:  1.57 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.50 (0.66), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 370 
 TYR   0.006   0.001   TYR A 464 
 PHE   0.007   0.001   PHE A 292 
 TRP   0.008   0.001   TRP A 186 
 HIS   0.000   0.000   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3512)
  covalent geometry    : angle       0.66408 ( 4788)
  hydrogen bonds       : bond        0.03710 (  284)
  hydrogen bonds       : angle       3.98842 (  846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 554.49 seconds
wall clock time: 10 minutes 13.72 seconds (613.72 seconds total)