Starting phenix.real_space_refine
on Wed Mar  5 14:21:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7abk_11698/03_2025/7abk_11698.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       2      5.16       5
     C     977      2.51       5
     N     289      2.21       5
     O     306      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 1574
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1574
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 3.60, per 1000 atoms: 2.29
  Number of scatterers: 1574
  At special positions: 0
  Unit cell: (69.6287, 180.364, 52.0118, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       2     16.00
     O     306      8.00
     N     289      7.00
     C     977      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: 0.40
  Conformation dependent library (CDL) restraints added in 184.6 milliseconds
  

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  378

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 0 sheets defined
      89.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 80
      removed outlier: 3.593A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A  29 " --> pdb=" O   PRO A  25 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 155
      removed outlier: 3.570A  pdb=" N   ALA A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLN A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   SER A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ALA A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN A 135 " --> pdb=" O   GLU A 131 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   LEU A 138 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN A 150 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 155 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 186
      removed outlier: 3.500A  pdb=" N   ASN A 186 " --> pdb=" O   ARG A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 216

    141 hydrogen bonds defined for protein.
    423 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: 0.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 558
        1.34 -     1.46: 133
        1.46 -     1.57: 895
        1.57 -     1.69: 0
        1.69 -     1.80: 4
  Bond restraints: 1590
  Sorted by residual:
  bond pdb=" N   LYS A 151 "
       pdb=" CA  LYS A 151 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.77e+00
  bond pdb=" N   ILE A 152 "
       pdb=" CA  ILE A 152 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.29e-02 6.01e+03 7.12e+00
  bond pdb=" N   PHE A  54 "
       pdb=" CA  PHE A  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 4.98e+00
  bond pdb=" N   GLU A 153 "
       pdb=" CA  GLU A 153 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.029 1.30e-02 5.92e+03 4.81e+00
  bond pdb=" CA  THR A  53 "
       pdb=" C   THR A  53 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.35e-02 5.49e+03 2.00e+00
  ... (remaining 1585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 2037
        1.41 -     2.82: 77
        2.82 -     4.23: 16
        4.23 -     5.64: 3
        5.64 -     7.05: 1
  Bond angle restraints: 2134
  Sorted by residual:
  angle pdb=" N   GLU A 153 "
        pdb=" CA  GLU A 153 "
        pdb=" C   GLU A 153 "
      ideal   model   delta    sigma   weight residual
     112.23  105.18    7.05 1.26e+00 6.30e-01 3.13e+01
  angle pdb=" N   PHE A  54 "
        pdb=" CA  PHE A  54 "
        pdb=" C   PHE A  54 "
      ideal   model   delta    sigma   weight residual
     111.07  106.74    4.33 1.07e+00 8.73e-01 1.64e+01
  angle pdb=" N   ALA A  52 "
        pdb=" CA  ALA A  52 "
        pdb=" C   ALA A  52 "
      ideal   model   delta    sigma   weight residual
     111.02  115.79   -4.77 1.22e+00 6.72e-01 1.53e+01
  angle pdb=" N   ILE A 152 "
        pdb=" CA  ILE A 152 "
        pdb=" C   ILE A 152 "
      ideal   model   delta    sigma   weight residual
     112.80  109.11    3.69 1.15e+00 7.56e-01 1.03e+01
  angle pdb=" C   THR A  53 "
        pdb=" CA  THR A  53 "
        pdb=" CB  THR A  53 "
      ideal   model   delta    sigma   weight residual
     110.67  105.27    5.40 1.92e+00 2.71e-01 7.91e+00
  ... (remaining 2129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 891
       17.40 -    34.80: 93
       34.80 -    52.20: 17
       52.20 -    69.60: 8
       69.60 -    87.00: 4
  Dihedral angle restraints: 1013
    sinusoidal: 436
      harmonic: 577
  Sorted by residual:
  dihedral pdb=" CA  ASP A 160 "
           pdb=" C   ASP A 160 "
           pdb=" N   ASN A 161 "
           pdb=" CA  ASN A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.23   15.77     0      5.00e+00 4.00e-02 9.94e+00
  dihedral pdb=" CA  LYS A 151 "
           pdb=" CB  LYS A 151 "
           pdb=" CG  LYS A 151 "
           pdb=" CD  LYS A 151 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.17  -55.83     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CA  LEU A 159 "
           pdb=" C   LEU A 159 "
           pdb=" N   ASP A 160 "
           pdb=" CA  ASP A 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.87   15.13     0      5.00e+00 4.00e-02 9.16e+00
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 186
       0.039 -    0.077: 39
       0.077 -    0.116: 9
       0.116 -    0.154: 1
       0.154 -    0.192: 1
  Chirality restraints: 236
  Sorted by residual:
  chirality pdb=" CA  ALA A  52 "
            pdb=" N   ALA A  52 "
            pdb=" C   ALA A  52 "
            pdb=" CB  ALA A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  ILE A 152 "
            pdb=" N   ILE A 152 "
            pdb=" C   ILE A 152 "
            pdb=" CB  ILE A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  PHE A  54 "
            pdb=" N   PHE A  54 "
            pdb=" C   PHE A  54 "
            pdb=" CB  PHE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.33e-01
  ... (remaining 233 not shown)

  Planarity restraints: 284
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 150 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.13e+00
        pdb=" C   GLN A 150 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLN A 150 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS A 151 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 188 "    0.016 5.00e-02 4.00e+02   2.41e-02 9.31e-01
        pdb=" N   PRO A 189 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 152 "   -0.004 2.00e-02 2.50e+03   8.67e-03 7.52e-01
        pdb=" C   ILE A 152 "    0.015 2.00e-02 2.50e+03
        pdb=" O   ILE A 152 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A 153 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 281 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 477
        2.83 -     3.35: 1780
        3.35 -     3.87: 2446
        3.87 -     4.38: 2475
        4.38 -     4.90: 4008
  Nonbonded interactions: 11186
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  26 "
            pdb=" CD1 LEU A 143 "
     model   vdw
     2.315 3.460
  nonbonded pdb=" O   SER A  96 "
            pdb=" OG  SER A  99 "
     model   vdw
     2.436 3.040
  nonbonded pdb=" N   GLU A  30 "
            pdb=" OE1 GLU A  30 "
     model   vdw
     2.443 3.120
  nonbonded pdb=" OD1 ASN A 161 "
            pdb=" OG  SER A 163 "
     model   vdw
     2.453 3.040
  nonbonded pdb=" NH1 ARG A  44 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.503 3.120
  ... (remaining 11181 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:             3.740
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.490
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   1590  Z= 0.281
  Angle     :  0.660   7.053   2134  Z= 0.437
  Chirality :  0.037   0.192    236
  Planarity :  0.003   0.024    284
  Dihedral  : 16.299  87.004    635
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.17 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.56), residues: 194
  helix:  0.77 (0.36), residues: 169
  sheet:  None (None), residues: 0
  loop :  0.20 (1.53), residues: 25

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.012   0.003   PHE A 168 
 TYR   0.004   0.001   TYR A 129 
 ARG   0.002   0.000   ARG A  45 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8538 (ttm170)
REVERT: A   58 GLU cc_start: 0.9103 (tt0) cc_final: 0.8547 (tm-30)
REVERT: A   62 ASP cc_start: 0.9021 (m-30) cc_final: 0.6966 (m-30)
REVERT: A  121 GLN cc_start: 0.8566 (mt0) cc_final: 0.8170 (tt0)
REVERT: A  127 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8493 (ttm-80)
REVERT: A  128 LYS cc_start: 0.8914 (tptm) cc_final: 0.8441 (ttpt)
REVERT: A  172 GLU cc_start: 0.8958 (tp30) cc_final: 0.8337 (tp30)
REVERT: A  174 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8218 (ttpt)
REVERT: A  177 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8642 (tm-30)
REVERT: A  179 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: A  195 LYS cc_start: 0.9568 (ttmt) cc_final: 0.8970 (tptp)
REVERT: A  198 GLN cc_start: 0.9465 (tt0) cc_final: 0.9051 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.2527
  time to fit residues: 21.5131
Evaluate side-chains
  55 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.100603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.081464 restraints weight = 3855.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.083694 restraints weight = 1745.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.085211 restraints weight = 1101.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1590  Z= 0.194
  Angle     :  0.564   5.263   2134  Z= 0.303
  Chirality :  0.030   0.104    236
  Planarity :  0.004   0.028    284
  Dihedral  :  5.853  55.007    220
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.52 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.58), residues: 194
  helix:  2.75 (0.37), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.99 (1.23), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.008   0.002   PHE A 168 
 TYR   0.009   0.002   TYR A 129 
 ARG   0.007   0.001   ARG A  70 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7650 (tpp) cc_final: 0.7288 (tpp)
REVERT: A   58 GLU cc_start: 0.8949 (tt0) cc_final: 0.8611 (tm-30)
REVERT: A   62 ASP cc_start: 0.8863 (m-30) cc_final: 0.7012 (m-30)
REVERT: A  106 LYS cc_start: 0.8831 (mttt) cc_final: 0.8621 (mtmm)
REVERT: A  121 GLN cc_start: 0.8553 (mt0) cc_final: 0.8251 (tt0)
REVERT: A  123 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8076 (pp30)
REVERT: A  128 LYS cc_start: 0.8909 (tptm) cc_final: 0.8506 (ttpt)
REVERT: A  174 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8321 (ttmt)
REVERT: A  179 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8409 (tm-30)
REVERT: A  195 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9125 (tptt)
REVERT: A  198 GLN cc_start: 0.9199 (tt0) cc_final: 0.8992 (tm-30)
REVERT: A  212 MET cc_start: 0.7976 (tpt) cc_final: 0.7111 (tpt)
  outliers start: 5
  outliers final: 3
  residues processed: 69
  average time/residue: 0.2460
  time to fit residues: 18.2130
Evaluate side-chains
  62 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.104432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.084908 restraints weight = 3825.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.087291 restraints weight = 1762.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.088941 restraints weight = 1096.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   1590  Z= 0.185
  Angle     :  0.573   6.756   2134  Z= 0.287
  Chirality :  0.030   0.109    236
  Planarity :  0.003   0.029    284
  Dihedral  :  5.280  49.593    220
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.60 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.57 (0.58), residues: 194
  helix:  3.42 (0.37), residues: 173
  sheet:  None (None), residues: 0
  loop : -1.14 (1.11), residues: 21

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.006   0.001   PHE A 168 
 TYR   0.010   0.001   TYR A 129 
 ARG   0.005   0.001   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7538 (tpp) cc_final: 0.7240 (tpp)
REVERT: A  121 GLN cc_start: 0.8542 (mt0) cc_final: 0.8161 (tt0)
REVERT: A  123 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8237 (pp30)
REVERT: A  128 LYS cc_start: 0.8809 (tptm) cc_final: 0.8363 (ttpt)
REVERT: A  179 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: A  195 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9076 (tptt)
REVERT: A  198 GLN cc_start: 0.9251 (tt0) cc_final: 0.9013 (tm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2331
  time to fit residues: 16.0876
Evaluate side-chains
  57 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.104979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.085207 restraints weight = 3897.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.087523 restraints weight = 1795.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.088978 restraints weight = 1129.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1590  Z= 0.167
  Angle     :  0.541   5.285   2134  Z= 0.277
  Chirality :  0.031   0.113    236
  Planarity :  0.003   0.023    284
  Dihedral  :  5.215  50.046    220
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.07 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.86 (0.57), residues: 194
  helix:  3.61 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.79 (1.17), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  71 
 HIS   0.001   0.001   HIS A 100 
 PHE   0.005   0.001   PHE A 168 
 TYR   0.010   0.001   TYR A 129 
 ARG   0.005   0.000   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7416 (tpp) cc_final: 0.7102 (tpp)
REVERT: A  121 GLN cc_start: 0.8567 (mt0) cc_final: 0.8198 (tt0)
REVERT: A  123 GLN cc_start: 0.8500 (tm130) cc_final: 0.8300 (pp30)
REVERT: A  128 LYS cc_start: 0.8844 (tptm) cc_final: 0.8303 (ttpt)
REVERT: A  154 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: A  179 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8345 (tm-30)
REVERT: A  195 LYS cc_start: 0.9561 (ttmt) cc_final: 0.9059 (tptt)
REVERT: A  198 GLN cc_start: 0.9228 (tt0) cc_final: 0.9002 (tm-30)
REVERT: A  200 GLU cc_start: 0.8947 (pp20) cc_final: 0.8612 (pp20)
  outliers start: 6
  outliers final: 5
  residues processed: 63
  average time/residue: 0.2071
  time to fit residues: 14.1625
Evaluate side-chains
  63 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.103695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.084457 restraints weight = 3903.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086703 restraints weight = 1814.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.088240 restraints weight = 1143.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1590  Z= 0.175
  Angle     :  0.554   6.864   2134  Z= 0.278
  Chirality :  0.032   0.120    236
  Planarity :  0.003   0.021    284
  Dihedral  :  5.241  52.836    220
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.69 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.80 (0.56), residues: 194
  helix:  3.57 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.80 (1.20), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.005   0.001   PHE A 168 
 TYR   0.009   0.001   TYR A 129 
 ARG   0.005   0.000   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7450 (tpp) cc_final: 0.7157 (tpp)
REVERT: A  121 GLN cc_start: 0.8573 (mt0) cc_final: 0.8220 (tt0)
REVERT: A  128 LYS cc_start: 0.8825 (tptm) cc_final: 0.8278 (ttpt)
REVERT: A  154 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: A  179 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8343 (tm-30)
REVERT: A  195 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9059 (tptt)
REVERT: A  198 GLN cc_start: 0.9235 (tt0) cc_final: 0.9032 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.2077
  time to fit residues: 13.5227
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.104198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.084921 restraints weight = 3952.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.086876 restraints weight = 1776.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088471 restraints weight = 1161.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   1590  Z= 0.166
  Angle     :  0.606  12.818   2134  Z= 0.289
  Chirality :  0.031   0.112    236
  Planarity :  0.003   0.024    284
  Dihedral  :  5.255  53.628    220
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 25.31 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.79 (0.56), residues: 194
  helix:  3.57 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.82 (1.22), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.005   0.001   PHE A 168 
 TYR   0.008   0.001   TYR A 129 
 ARG   0.006   0.000   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7497 (tpp) cc_final: 0.7188 (tpp)
REVERT: A  124 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9024 (tppp)
REVERT: A  128 LYS cc_start: 0.8793 (tptm) cc_final: 0.8179 (ttpt)
REVERT: A  179 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: A  195 LYS cc_start: 0.9569 (ttmt) cc_final: 0.9057 (tptt)
REVERT: A  198 GLN cc_start: 0.9253 (tt0) cc_final: 0.9046 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 58
  average time/residue: 0.2087
  time to fit residues: 13.1480
Evaluate side-chains
  58 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 13 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6100

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.106722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.087357 restraints weight = 3930.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.089762 restraints weight = 1773.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.091291 restraints weight = 1110.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   1590  Z= 0.157
  Angle     :  0.629  12.798   2134  Z= 0.297
  Chirality :  0.031   0.114    236
  Planarity :  0.003   0.025    284
  Dihedral  :  5.113  51.687    220
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 27.16 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.82 (0.56), residues: 194
  helix:  3.61 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.97 (1.19), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.005   0.001   PHE A 168 
 TYR   0.008   0.001   TYR A 129 
 ARG   0.006   0.000   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   42 GLU cc_start: 0.9021 (tp30) cc_final: 0.8783 (mm-30)
REVERT: A  128 LYS cc_start: 0.8771 (tptm) cc_final: 0.8166 (ttpt)
REVERT: A  179 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: A  195 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9044 (tptt)
REVERT: A  198 GLN cc_start: 0.9250 (tt0) cc_final: 0.9036 (tm-30)
REVERT: A  200 GLU cc_start: 0.9002 (pp20) cc_final: 0.8674 (pp20)
  outliers start: 5
  outliers final: 4
  residues processed: 59
  average time/residue: 0.2086
  time to fit residues: 13.3665
Evaluate side-chains
  57 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.106543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.087125 restraints weight = 3844.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.089511 restraints weight = 1734.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.091094 restraints weight = 1073.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1590  Z= 0.156
  Angle     :  0.627   7.257   2134  Z= 0.298
  Chirality :  0.032   0.151    236
  Planarity :  0.003   0.022    284
  Dihedral  :  5.159  52.931    220
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 28.40 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.74 (0.56), residues: 194
  helix:  3.56 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.09 (1.17), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.004   0.001   PHE A 168 
 TYR   0.008   0.001   TYR A 129 
 ARG   0.006   0.000   ARG A 127 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   42 GLU cc_start: 0.9052 (tp30) cc_final: 0.8807 (mm-30)
REVERT: A  128 LYS cc_start: 0.8740 (tptm) cc_final: 0.8109 (ttpt)
REVERT: A  179 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: A  195 LYS cc_start: 0.9565 (ttmt) cc_final: 0.9033 (tptt)
REVERT: A  198 GLN cc_start: 0.9264 (tt0) cc_final: 0.9055 (tm-30)
REVERT: A  200 GLU cc_start: 0.9035 (pp20) cc_final: 0.8702 (pp20)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.2366
  time to fit residues: 14.3016
Evaluate side-chains
  57 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.105653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086417 restraints weight = 3893.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.088759 restraints weight = 1773.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.090283 restraints weight = 1096.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.5195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1590  Z= 0.179
  Angle     :  0.655   8.660   2134  Z= 0.311
  Chirality :  0.032   0.133    236
  Planarity :  0.003   0.028    284
  Dihedral  :  5.195  54.314    220
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.16 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.71 (0.56), residues: 194
  helix:  3.55 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.16 (1.15), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.004   0.001   PHE A 168 
 TYR   0.010   0.001   TYR A 129 
 ARG   0.008   0.001   ARG A  59 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   42 GLU cc_start: 0.9068 (tp30) cc_final: 0.8820 (mm-30)
REVERT: A  124 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9055 (tppp)
REVERT: A  128 LYS cc_start: 0.8693 (tptm) cc_final: 0.8077 (ttpt)
REVERT: A  133 LYS cc_start: 0.9419 (ttmm) cc_final: 0.9102 (ttmm)
REVERT: A  179 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: A  195 LYS cc_start: 0.9566 (ttmt) cc_final: 0.9038 (tptt)
REVERT: A  200 GLU cc_start: 0.9033 (pp20) cc_final: 0.8707 (pp20)
  outliers start: 6
  outliers final: 5
  residues processed: 58
  average time/residue: 0.2138
  time to fit residues: 13.4750
Evaluate side-chains
  57 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0040
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.107846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088463 restraints weight = 3936.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.090819 restraints weight = 1764.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.092432 restraints weight = 1090.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.5447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1590  Z= 0.194
  Angle     :  0.713   9.585   2134  Z= 0.339
  Chirality :  0.033   0.146    236
  Planarity :  0.003   0.033    284
  Dihedral  :  5.109  52.396    220
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 29.01 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.66 (0.56), residues: 194
  helix:  3.52 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.20 (1.15), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.004   0.001   PHE A 168 
 TYR   0.009   0.001   TYR A 129 
 ARG   0.007   0.001   ARG A  59 

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9099 (tppp)
REVERT: A  128 LYS cc_start: 0.8691 (tptm) cc_final: 0.8019 (ttpt)
REVERT: A  133 LYS cc_start: 0.9414 (ttmm) cc_final: 0.9102 (ttmm)
REVERT: A  179 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: A  195 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9057 (tptt)
REVERT: A  200 GLU cc_start: 0.9076 (pp20) cc_final: 0.8699 (pp20)
  outliers start: 5
  outliers final: 5
  residues processed: 59
  average time/residue: 0.2328
  time to fit residues: 14.8790
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.107235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.087508 restraints weight = 3997.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.089912 restraints weight = 1806.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.091516 restraints weight = 1107.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.5490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1590  Z= 0.197
  Angle     :  0.729   9.285   2134  Z= 0.338
  Chirality :  0.033   0.146    236
  Planarity :  0.003   0.032    284
  Dihedral  :  5.101  52.510    220
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 30.86 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.70 (0.56), residues: 194
  helix:  3.55 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.20 (1.15), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 
 PHE   0.003   0.001   PHE A 168 
 TYR   0.009   0.001   TYR A 129 
 ARG   0.007   0.001   ARG A  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1238.26 seconds
wall clock time: 22 minutes 14.85 seconds (1334.85 seconds total)