Starting phenix.real_space_refine
on Tue Mar  3 11:04:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v48_31703/03_2026/7v48_31703.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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: 3
    Type Number    sf(0)   Gaussians
     C    1626      2.51       5
     N     450      2.21       5
     O     522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2598
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 433
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    A, E, C, F, D
  Time building chain proxies: 0.33, per 1000 atoms: 0.13
  Number of scatterers: 2598
  At special positions: 0
  Unit cell: (104.94, 110.24, 32.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     522      8.00
     N     450      7.00
     C    1626      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: 0.11
  Conformation dependent library (CDL) restraints added in 67.6 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 40
      removed outlier: 6.719A  pdb=" N   TYR B  39 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50
      removed outlier: 6.501A  pdb=" N   VAL B  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'E' and resid 75 through 79
      removed outlier: 6.608A  pdb=" N   ALA B  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   GLN F  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ALA B  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 82 through 83
      removed outlier: 6.541A  pdb=" N   VAL B  82 " --> pdb=" O   GLU F  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40
      removed outlier: 6.748A  pdb=" N   TYR A  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 50
      removed outlier: 6.513A  pdb=" N   VAL A  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79
      removed outlier: 6.603A  pdb=" N   ALA A  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   GLN D  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ALA A  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83
      removed outlier: 6.549A  pdb=" N   VAL A  82 " --> pdb=" O   GLU D  83 " (cutoff:3.500A)

    19 hydrogen bonds defined for protein.
    57 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: 0.20

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 456
        1.29 -     1.36: 408
        1.36 -     1.42: 102
        1.42 -     1.49: 426
        1.49 -     1.55: 1218
  Bond restraints: 2610
  Sorted by residual:
  bond pdb=" CA  ALA D  90 "
       pdb=" C   ALA D  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.10e-02 8.26e+03 4.74e-01
  bond pdb=" CA  ALA F  90 "
       pdb=" C   ALA F  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.10e-02 8.26e+03 4.74e-01
  bond pdb=" CA  ALA A  90 "
       pdb=" C   ALA A  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.10e-02 8.26e+03 4.70e-01
  bond pdb=" CA  ALA B  90 "
       pdb=" C   ALA B  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.10e-02 8.26e+03 4.14e-01
  bond pdb=" CA  ALA E  90 "
       pdb=" C   ALA E  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.10e-02 8.26e+03 4.09e-01
  ... (remaining 2605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.55: 2848
        0.55 -     1.10: 539
        1.10 -     1.65: 103
        1.65 -     2.21: 32
        2.21 -     2.76: 6
  Bond angle restraints: 3528
  Sorted by residual:
  angle pdb=" CA  ALA F  90 "
        pdb=" C   ALA F  90 "
        pdb=" N   ALA F  91 "
      ideal   model   delta    sigma   weight residual
     114.76  116.75   -1.99 1.14e+00 7.69e-01 3.05e+00
  angle pdb=" CA  ALA D  90 "
        pdb=" C   ALA D  90 "
        pdb=" N   ALA D  91 "
      ideal   model   delta    sigma   weight residual
     114.76  116.71   -1.95 1.14e+00 7.69e-01 2.94e+00
  angle pdb=" CA  ALA C  90 "
        pdb=" C   ALA C  90 "
        pdb=" N   ALA C  91 "
      ideal   model   delta    sigma   weight residual
     114.76  116.69   -1.93 1.14e+00 7.69e-01 2.86e+00
  angle pdb=" CA  ALA A  90 "
        pdb=" C   ALA A  90 "
        pdb=" N   ALA A  91 "
      ideal   model   delta    sigma   weight residual
     114.76  116.69   -1.93 1.14e+00 7.69e-01 2.86e+00
  angle pdb=" CA  ALA E  90 "
        pdb=" C   ALA E  90 "
        pdb=" N   ALA E  91 "
      ideal   model   delta    sigma   weight residual
     114.76  116.68   -1.92 1.14e+00 7.69e-01 2.84e+00
  ... (remaining 3523 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.21: 1350
       13.21 -    26.41: 120
       26.41 -    39.62: 36
       39.62 -    52.82: 0
       52.82 -    66.03: 12
  Dihedral angle restraints: 1518
    sinusoidal: 504
      harmonic: 1014
  Sorted by residual:
  dihedral pdb=" CA  ASP B  98 "
           pdb=" CB  ASP B  98 "
           pdb=" CG  ASP B  98 "
           pdb=" OD1 ASP B  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.45   59.45     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  ASP F  98 "
           pdb=" CB  ASP F  98 "
           pdb=" CG  ASP F  98 "
           pdb=" OD1 ASP F  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.44   59.44     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  ASP C  98 "
           pdb=" CB  ASP C  98 "
           pdb=" CG  ASP C  98 "
           pdb=" OD1 ASP C  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.41   59.41     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 1515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 227
       0.026 -    0.053: 128
       0.053 -    0.079: 35
       0.079 -    0.106: 37
       0.106 -    0.132: 35
  Chirality restraints: 462
  Sorted by residual:
  chirality pdb=" CA  VAL C  66 "
            pdb=" N   VAL C  66 "
            pdb=" C   VAL C  66 "
            pdb=" CB  VAL C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL D  66 "
            pdb=" N   VAL D  66 "
            pdb=" C   VAL D  66 "
            pdb=" CB  VAL D  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL F  66 "
            pdb=" N   VAL F  66 "
            pdb=" C   VAL F  66 "
            pdb=" CB  VAL F  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 459 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  68 "    0.003 2.00e-02 2.50e+03   6.10e-03 3.72e-01
        pdb=" C   GLY B  68 "   -0.011 2.00e-02 2.50e+03
        pdb=" O   GLY B  68 "    0.004 2.00e-02 2.50e+03
        pdb=" N   ALA B  69 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  68 "   -0.003 2.00e-02 2.50e+03   6.08e-03 3.70e-01
        pdb=" C   GLY A  68 "    0.011 2.00e-02 2.50e+03
        pdb=" O   GLY A  68 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   ALA A  69 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  68 "   -0.003 2.00e-02 2.50e+03   6.04e-03 3.65e-01
        pdb=" C   GLY D  68 "    0.010 2.00e-02 2.50e+03
        pdb=" O   GLY D  68 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   ALA D  69 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 716
        2.82 -     3.34: 2357
        3.34 -     3.86: 3650
        3.86 -     4.38: 4096
        4.38 -     4.90: 8597
  Nonbonded interactions: 19416
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN E  62 "
            pdb=" OG1 THR E  64 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NE2 GLN C  62 "
            pdb=" OG1 THR C  64 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NE2 GLN F  62 "
            pdb=" OG1 THR F  64 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NE2 GLN B  62 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NE2 GLN D  62 "
            pdb=" OG1 THR D  64 "
     model   vdw
     2.296 3.120
  ... (remaining 19411 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'E'
  selection = chain 'C'
  selection = chain 'F'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.170
  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:5.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
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      :  0.002   0.009   2610  Z= 0.109
  Angle     :  0.484   2.756   3528  Z= 0.293
  Chirality :  0.051   0.132    462
  Planarity :  0.001   0.006    438
  Dihedral  : 12.912  66.027    882
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.61 (0.29), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.22), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR D  39 
 PHE   0.005   0.001   PHE C  94 
 HIS   0.001   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 ( 2610)
  covalent geometry    : angle       0.48380 ( 3528)
  hydrogen bonds       : bond        0.18944 (   19)
  hydrogen bonds       : angle       8.14965 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.054 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.6694 (tt0) cc_final: 0.5943 (tp30)
REVERT: A   46 GLU cc_start: 0.6393 (tt0) cc_final: 0.5828 (tp30)
REVERT: A   57 GLU cc_start: 0.7223 (tt0) cc_final: 0.6981 (mt-10)
REVERT: E   43 LYS cc_start: 0.7369 (tttt) cc_final: 0.7013 (mtpp)
REVERT: E   46 GLU cc_start: 0.7164 (tt0) cc_final: 0.6744 (tt0)
REVERT: C   43 LYS cc_start: 0.7382 (tttt) cc_final: 0.7090 (mtpm)
REVERT: C   46 GLU cc_start: 0.6823 (tt0) cc_final: 0.6023 (tp30)
REVERT: F   43 LYS cc_start: 0.7784 (tttt) cc_final: 0.7579 (ttmm)
REVERT: F   46 GLU cc_start: 0.6978 (tt0) cc_final: 0.6701 (tt0)
REVERT: D   46 GLU cc_start: 0.7070 (tt0) cc_final: 0.6471 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.3395
  time to fit residues: 23.3724
Evaluate side-chains
  47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
E  79 GLN
C  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.159262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.116141 restraints weight = 2910.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.83
r_work: 0.3796 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   2610  Z= 0.237
  Angle     :  0.582   3.652   3528  Z= 0.336
  Chirality :  0.051   0.124    462
  Planarity :  0.003   0.008    438
  Dihedral  :  5.200  15.519    378
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.49 %
    Favored  : 79.51 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  :  9.85 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.41 (0.30), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.12 (0.23), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.004   TYR B  39 
 PHE   0.007   0.002   PHE A  94 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 2610)
  covalent geometry    : angle       0.58230 ( 3528)
  hydrogen bonds       : bond        0.02826 (   19)
  hydrogen bonds       : angle       5.06551 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.060 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7475 (tt0) cc_final: 0.6741 (tp30)
REVERT: B   65 ASN cc_start: 0.7315 (t0) cc_final: 0.7113 (t0)
REVERT: A   46 GLU cc_start: 0.7364 (tt0) cc_final: 0.6353 (tm-30)
REVERT: A   92 THR cc_start: 0.7562 (m) cc_final: 0.7237 (p)
REVERT: E   43 LYS cc_start: 0.7958 (tttt) cc_final: 0.7655 (mtpm)
REVERT: E   46 GLU cc_start: 0.7893 (tt0) cc_final: 0.6955 (tm-30)
REVERT: E   92 THR cc_start: 0.7619 (m) cc_final: 0.7125 (p)
REVERT: C   46 GLU cc_start: 0.7685 (tt0) cc_final: 0.6899 (tp30)
REVERT: F   46 GLU cc_start: 0.7696 (tt0) cc_final: 0.7476 (tt0)
REVERT: F   57 GLU cc_start: 0.8142 (tt0) cc_final: 0.7919 (tt0)
REVERT: D   46 GLU cc_start: 0.7934 (tt0) cc_final: 0.7154 (tp30)
REVERT: D   62 GLN cc_start: 0.7402 (tp40) cc_final: 0.7075 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 60
  average time/residue: 0.4161
  time to fit residues: 25.6543
Evaluate side-chains
  49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0570
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.6242

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.164189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.120287 restraints weight = 2852.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.86
r_work: 0.3845 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2610  Z= 0.110
  Angle     :  0.473   4.087   3528  Z= 0.263
  Chirality :  0.050   0.127    462
  Planarity :  0.002   0.005    438
  Dihedral  :  4.513  13.005    378
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 12.50 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.92 (0.32), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.24), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR B  39 
 PHE   0.005   0.001   PHE A  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 2610)
  covalent geometry    : angle       0.47331 ( 3528)
  hydrogen bonds       : bond        0.01723 (   19)
  hydrogen bonds       : angle       4.16712 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.116 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7222 (tt0) cc_final: 0.6538 (tp30)
REVERT: B   65 ASN cc_start: 0.7156 (t0) cc_final: 0.6927 (t0)
REVERT: A   46 GLU cc_start: 0.7122 (tt0) cc_final: 0.6110 (tp30)
REVERT: A   92 THR cc_start: 0.7394 (m) cc_final: 0.7108 (p)
REVERT: E   43 LYS cc_start: 0.7682 (tttt) cc_final: 0.7321 (mtpm)
REVERT: E   46 GLU cc_start: 0.7539 (tt0) cc_final: 0.6602 (tp30)
REVERT: E   92 THR cc_start: 0.7559 (m) cc_final: 0.7063 (p)
REVERT: C   46 GLU cc_start: 0.7579 (tt0) cc_final: 0.6523 (tp30)
REVERT: F   46 GLU cc_start: 0.7364 (tt0) cc_final: 0.7109 (tt0)
REVERT: F   92 THR cc_start: 0.7975 (m) cc_final: 0.7487 (p)
REVERT: D   46 GLU cc_start: 0.7632 (tt0) cc_final: 0.6976 (tp30)
REVERT: D   62 GLN cc_start: 0.7405 (tp40) cc_final: 0.7031 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 57
  average time/residue: 0.4010
  time to fit residues: 23.5226
Evaluate side-chains
  47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0570
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    2.8106

-------------------------------------------------------------------------------
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 = 0.4467 r_free = 0.4467 target = 0.161663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.117680 restraints weight = 2859.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.86
r_work: 0.3819 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2610  Z= 0.171
  Angle     :  0.511   3.784   3528  Z= 0.289
  Chirality :  0.049   0.125    462
  Planarity :  0.002   0.006    438
  Dihedral  :  4.645  14.804    378
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.58 %
    Favored  : 81.42 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 12.88 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.32), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.71 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR C  39 
 PHE   0.006   0.001   PHE A  94 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2610)
  covalent geometry    : angle       0.51066 ( 3528)
  hydrogen bonds       : bond        0.01926 (   19)
  hydrogen bonds       : angle       4.10667 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.096 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7272 (tt0) cc_final: 0.6592 (tp30)
REVERT: B   65 ASN cc_start: 0.7189 (t0) cc_final: 0.6966 (t0)
REVERT: A   46 GLU cc_start: 0.7179 (tt0) cc_final: 0.6216 (tm-30)
REVERT: A   92 THR cc_start: 0.7399 (m) cc_final: 0.7175 (p)
REVERT: E   43 LYS cc_start: 0.7769 (tttt) cc_final: 0.7528 (mtpm)
REVERT: E   46 GLU cc_start: 0.7652 (tt0) cc_final: 0.6698 (tp30)
REVERT: E   92 THR cc_start: 0.7595 (m) cc_final: 0.7109 (p)
REVERT: C   46 GLU cc_start: 0.7667 (tt0) cc_final: 0.6791 (tp30)
REVERT: F   46 GLU cc_start: 0.7401 (tt0) cc_final: 0.7165 (tt0)
REVERT: F   92 THR cc_start: 0.7974 (m) cc_final: 0.7514 (p)
REVERT: D   43 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7862 (mtpp)
REVERT: D   46 GLU cc_start: 0.7699 (tt0) cc_final: 0.7030 (tp30)
REVERT: D   62 GLN cc_start: 0.7308 (tp40) cc_final: 0.7050 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 54
  average time/residue: 0.4471
  time to fit residues: 24.7421
Evaluate side-chains
  48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.162790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.118909 restraints weight = 2774.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 2.84
r_work: 0.3840 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2610  Z= 0.157
  Angle     :  0.509   4.046   3528  Z= 0.285
  Chirality :  0.049   0.125    462
  Planarity :  0.002   0.006    438
  Dihedral  :  4.613  14.932    378
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.85 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.91 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.80 (0.33), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR B  39 
 PHE   0.006   0.001   PHE A  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 2610)
  covalent geometry    : angle       0.50894 ( 3528)
  hydrogen bonds       : bond        0.01722 (   19)
  hydrogen bonds       : angle       3.98517 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7274 (tt0) cc_final: 0.6585 (tp30)
REVERT: B   65 ASN cc_start: 0.7264 (t0) cc_final: 0.6974 (t0)
REVERT: A   46 GLU cc_start: 0.7181 (tt0) cc_final: 0.6166 (tm-30)
REVERT: A   92 THR cc_start: 0.7381 (m) cc_final: 0.7159 (p)
REVERT: E   43 LYS cc_start: 0.7734 (tttt) cc_final: 0.7481 (mtpm)
REVERT: E   46 GLU cc_start: 0.7621 (tt0) cc_final: 0.6624 (tp30)
REVERT: E   92 THR cc_start: 0.7602 (m) cc_final: 0.7124 (p)
REVERT: C   46 GLU cc_start: 0.7661 (tt0) cc_final: 0.6772 (tp30)
REVERT: F   46 GLU cc_start: 0.7404 (tt0) cc_final: 0.7158 (tt0)
REVERT: F   92 THR cc_start: 0.7961 (m) cc_final: 0.7516 (p)
REVERT: D   46 GLU cc_start: 0.7678 (tt0) cc_final: 0.7009 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 49
  average time/residue: 0.4894
  time to fit residues: 24.6592
Evaluate side-chains
  45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   72 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0270
   chunk 2 optimal weight:   10.0000
   overall best weight:    4.5644

-------------------------------------------------------------------------------
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 = 0.4443 r_free = 0.4443 target = 0.159092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.115863 restraints weight = 2866.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 2.88
r_work: 0.3798 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2610  Z= 0.265
  Angle     :  0.623   4.463   3528  Z= 0.355
  Chirality :  0.051   0.123    462
  Planarity :  0.003   0.011    438
  Dihedral  :  5.235  15.966    378
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.68 %
    Favored  : 77.32 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.91 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.17 (0.31), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.24), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.004   TYR D  39 
 PHE   0.009   0.002   PHE A  94 
 HIS   0.003   0.002   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 2610)
  covalent geometry    : angle       0.62270 ( 3528)
  hydrogen bonds       : bond        0.02486 (   19)
  hydrogen bonds       : angle       4.30692 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.115 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7320 (tt0) cc_final: 0.6604 (tp30)
REVERT: B   65 ASN cc_start: 0.7298 (t0) cc_final: 0.7033 (t0)
REVERT: A   46 GLU cc_start: 0.7361 (tt0) cc_final: 0.6378 (tm-30)
REVERT: E   43 LYS cc_start: 0.7867 (tttt) cc_final: 0.7460 (mtpm)
REVERT: E   46 GLU cc_start: 0.7809 (tt0) cc_final: 0.6787 (tp30)
REVERT: E   54 THR cc_start: 0.8646 (m) cc_final: 0.8444 (m)
REVERT: E   92 THR cc_start: 0.7576 (m) cc_final: 0.7132 (p)
REVERT: C   46 GLU cc_start: 0.7569 (tt0) cc_final: 0.6894 (tp30)
REVERT: C   57 GLU cc_start: 0.7912 (tt0) cc_final: 0.7534 (tt0)
REVERT: F   46 GLU cc_start: 0.7554 (tt0) cc_final: 0.6910 (tm-30)
REVERT: F   92 THR cc_start: 0.7936 (m) cc_final: 0.7531 (p)
REVERT: D   43 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7887 (mtpp)
REVERT: D   46 GLU cc_start: 0.7681 (tt0) cc_final: 0.7041 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 51
  average time/residue: 0.4483
  time to fit residues: 23.5225
Evaluate side-chains
  49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.164923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.121634 restraints weight = 2778.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.88
r_work: 0.3867 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2610  Z= 0.116
  Angle     :  0.480   4.625   3528  Z= 0.266
  Chirality :  0.050   0.134    462
  Planarity :  0.002   0.007    438
  Dihedral  :  4.539  14.560    378
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.30 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 14.77 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.74 (0.33), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR B  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2610)
  covalent geometry    : angle       0.47990 ( 3528)
  hydrogen bonds       : bond        0.01439 (   19)
  hydrogen bonds       : angle       3.84975 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7339 (tt0) cc_final: 0.6638 (tp30)
REVERT: B   65 ASN cc_start: 0.7229 (t0) cc_final: 0.6935 (t0)
REVERT: A   46 GLU cc_start: 0.7155 (tt0) cc_final: 0.6155 (tm-30)
REVERT: E   43 LYS cc_start: 0.7676 (tttt) cc_final: 0.7384 (mtpm)
REVERT: E   46 GLU cc_start: 0.7636 (tt0) cc_final: 0.6644 (tp30)
REVERT: E   92 THR cc_start: 0.7558 (m) cc_final: 0.7098 (p)
REVERT: C   46 GLU cc_start: 0.7605 (tt0) cc_final: 0.6667 (tp30)
REVERT: C   57 GLU cc_start: 0.7861 (tt0) cc_final: 0.7382 (tt0)
REVERT: F   46 GLU cc_start: 0.7430 (tt0) cc_final: 0.7180 (tt0)
REVERT: F   92 THR cc_start: 0.7935 (m) cc_final: 0.7541 (p)
REVERT: D   43 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7787 (mtpp)
REVERT: D   46 GLU cc_start: 0.7536 (tt0) cc_final: 0.6944 (tp30)
  outliers start: 12
  outliers final: 9
  residues processed: 54
  average time/residue: 0.4871
  time to fit residues: 27.0440
Evaluate side-chains
  47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0000
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 13 optimal weight:    0.4980
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.0988

-------------------------------------------------------------------------------
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 = 0.4557 r_free = 0.4557 target = 0.168348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.124348 restraints weight = 2778.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.87
r_work: 0.3925 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2610  Z= 0.092
  Angle     :  0.448   4.698   3528  Z= 0.243
  Chirality :  0.049   0.125    462
  Planarity :  0.001   0.005    438
  Dihedral  :  4.049  12.058    378
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.39 %
    Favored  : 86.61 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.91 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.41 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR D  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 2610)
  covalent geometry    : angle       0.44806 ( 3528)
  hydrogen bonds       : bond        0.01053 (   19)
  hydrogen bonds       : angle       3.55312 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7272 (tt0) cc_final: 0.6587 (tp30)
REVERT: A   46 GLU cc_start: 0.7222 (tt0) cc_final: 0.6126 (tm-30)
REVERT: E   43 LYS cc_start: 0.7729 (tttt) cc_final: 0.7460 (mtpm)
REVERT: E   46 GLU cc_start: 0.7578 (tt0) cc_final: 0.6595 (tp30)
REVERT: E   92 THR cc_start: 0.7527 (m) cc_final: 0.6946 (p)
REVERT: C   46 GLU cc_start: 0.7616 (tt0) cc_final: 0.6666 (tp30)
REVERT: C   57 GLU cc_start: 0.7857 (tt0) cc_final: 0.7390 (tt0)
REVERT: F   46 GLU cc_start: 0.7384 (tt0) cc_final: 0.7128 (tt0)
REVERT: F   92 THR cc_start: 0.7924 (m) cc_final: 0.7502 (p)
REVERT: D   46 GLU cc_start: 0.7492 (tt0) cc_final: 0.6917 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 51
  average time/residue: 0.4605
  time to fit residues: 24.1666
Evaluate side-chains
  46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0030
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.4796

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.164179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.120426 restraints weight = 2876.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.91
r_work: 0.3858 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2610  Z= 0.160
  Angle     :  0.520   5.115   3528  Z= 0.287
  Chirality :  0.049   0.123    462
  Planarity :  0.002   0.006    438
  Dihedral  :  4.440  13.824    378
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.57 %
    Favored  : 84.43 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.94 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.48 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR D  39 
 PHE   0.005   0.001   PHE E  94 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 2610)
  covalent geometry    : angle       0.52008 ( 3528)
  hydrogen bonds       : bond        0.01491 (   19)
  hydrogen bonds       : angle       3.71457 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.097 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7272 (tt0) cc_final: 0.6595 (tp30)
REVERT: B   65 ASN cc_start: 0.7233 (t0) cc_final: 0.6942 (t0)
REVERT: A   46 GLU cc_start: 0.7193 (tt0) cc_final: 0.6162 (tm-30)
REVERT: E   43 LYS cc_start: 0.7726 (tttt) cc_final: 0.7375 (mtpm)
REVERT: E   46 GLU cc_start: 0.7709 (tt0) cc_final: 0.6669 (tp30)
REVERT: E   92 THR cc_start: 0.7557 (m) cc_final: 0.7104 (p)
REVERT: C   46 GLU cc_start: 0.7669 (tt0) cc_final: 0.6764 (tp30)
REVERT: C   57 GLU cc_start: 0.7830 (tt0) cc_final: 0.7324 (tt0)
REVERT: F   46 GLU cc_start: 0.7453 (tt0) cc_final: 0.7209 (tt0)
REVERT: F   92 THR cc_start: 0.7950 (m) cc_final: 0.7533 (p)
REVERT: D   46 GLU cc_start: 0.7601 (tt0) cc_final: 0.6984 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 47
  average time/residue: 0.4980
  time to fit residues: 24.0376
Evaluate side-chains
  43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0070
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.9802

-------------------------------------------------------------------------------
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 = 0.4529 r_free = 0.4529 target = 0.165838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.122289 restraints weight = 2807.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.89
r_work: 0.3881 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2610  Z= 0.133
  Angle     :  0.502   5.550   3528  Z= 0.273
  Chirality :  0.049   0.124    462
  Planarity :  0.002   0.005    438
  Dihedral  :  4.349  13.428    378
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.75 %
    Favored  : 85.25 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.32 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.41 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR D  39 
 PHE   0.005   0.001   PHE E  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2610)
  covalent geometry    : angle       0.50181 ( 3528)
  hydrogen bonds       : bond        0.01318 (   19)
  hydrogen bonds       : angle       3.64743 (   57)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.060 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7334 (tt0) cc_final: 0.6638 (tp30)
REVERT: A   46 GLU cc_start: 0.7158 (tt0) cc_final: 0.6176 (tm-30)
REVERT: E   43 LYS cc_start: 0.7701 (tttt) cc_final: 0.7348 (mtpm)
REVERT: E   46 GLU cc_start: 0.7657 (tt0) cc_final: 0.6642 (tp30)
REVERT: E   92 THR cc_start: 0.7554 (m) cc_final: 0.6973 (p)
REVERT: C   46 GLU cc_start: 0.7614 (tt0) cc_final: 0.6697 (tp30)
REVERT: C   57 GLU cc_start: 0.7814 (tt0) cc_final: 0.7374 (tt0)
REVERT: F   46 GLU cc_start: 0.7407 (tt0) cc_final: 0.7161 (tt0)
REVERT: F   92 THR cc_start: 0.7943 (m) cc_final: 0.7532 (p)
REVERT: D   46 GLU cc_start: 0.7531 (tt0) cc_final: 0.6912 (tp30)
  outliers start: 6
  outliers final: 6
  residues processed: 44
  average time/residue: 0.5052
  time to fit residues: 22.8397
Evaluate side-chains
  44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    0.0060
   chunk 32 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0970
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.4198

-------------------------------------------------------------------------------
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 = 0.4548 r_free = 0.4548 target = 0.167265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.123366 restraints weight = 2787.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 2.88
r_work: 0.3912 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2610  Z= 0.107
  Angle     :  0.465   5.463   3528  Z= 0.252
  Chirality :  0.049   0.122    462
  Planarity :  0.001   0.006    438
  Dihedral  :  4.097  12.057    378
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.70 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.29 (0.36), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR D  39 
 PHE   0.004   0.001   PHE E  94 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 2610)
  covalent geometry    : angle       0.46489 ( 3528)
  hydrogen bonds       : bond        0.01083 (   19)
  hydrogen bonds       : angle       3.52962 (   57)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1029.06 seconds
wall clock time: 18 minutes 14.49 seconds (1094.49 seconds total)