Starting phenix.real_space_refine
on Tue Mar  3 12:08:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2026/6zrq_11382.map"
  }
  resolution = 3.9
  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=   0.001
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
     C    1272      2.51       5
     N     360      2.21       5
     O     408      1.98       5
     H    1908      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 3948
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 329
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 0.46, per 1000 atoms: 0.12
  Number of scatterers: 3948
  At special positions: 0
  Unit cell: (50.055, 79.875, 44.73, 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)
     O     408      8.00
     N     360      7.00
     C    1272      6.00
     H    1908      1.00
    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: 0.39
  Conformation dependent library (CDL) restraints added in 98.8 milliseconds
  

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  480

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        0.83 -     0.97: 1753
        0.97 -     1.12: 155
        1.12 -     1.26: 324
        1.26 -     1.40: 612
        1.40 -     1.54: 1140
  Bond restraints: 3984
  Sorted by residual:
  bond pdb=" N   TYC H  37 "
       pdb=" H   TYC H  37 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.25e+01
  bond pdb=" N   TYC L  37 "
       pdb=" H   TYC L  37 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.23e+01
  bond pdb=" N   TYC A  37 "
       pdb=" H   TYC A  37 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.23e+01
  bond pdb=" N   TYC K  37 "
       pdb=" H   TYC K  37 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.22e+01
  bond pdb=" N   TYC C  37 "
       pdb=" H   TYC C  37 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.21e+01
  ... (remaining 3979 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 6815
        2.35 -     4.71: 187
        4.71 -     7.06: 6
        7.06 -     9.42: 0
        9.42 -    11.77: 12
  Bond angle restraints: 7020
  Sorted by residual:
  angle pdb=" CA  LEU I  16 "
        pdb=" CB  LEU I  16 "
        pdb=" CG  LEU I  16 "
      ideal   model   delta    sigma   weight residual
     116.30  128.07  -11.77 3.50e+00 8.16e-02 1.13e+01
  angle pdb=" CA  LEU K  16 "
        pdb=" CB  LEU K  16 "
        pdb=" CG  LEU K  16 "
      ideal   model   delta    sigma   weight residual
     116.30  128.05  -11.75 3.50e+00 8.16e-02 1.13e+01
  angle pdb=" CA  LEU C  16 "
        pdb=" CB  LEU C  16 "
        pdb=" CG  LEU C  16 "
      ideal   model   delta    sigma   weight residual
     116.30  128.04  -11.74 3.50e+00 8.16e-02 1.13e+01
  angle pdb=" CA  LEU D  16 "
        pdb=" CB  LEU D  16 "
        pdb=" CG  LEU D  16 "
      ideal   model   delta    sigma   weight residual
     116.30  128.03  -11.73 3.50e+00 8.16e-02 1.12e+01
  angle pdb=" CA  LEU F  16 "
        pdb=" CB  LEU F  16 "
        pdb=" CG  LEU F  16 "
      ideal   model   delta    sigma   weight residual
     116.30  128.03  -11.73 3.50e+00 8.16e-02 1.12e+01
  ... (remaining 7015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.47: 1500
       12.47 -    24.93: 312
       24.93 -    37.40: 36
       37.40 -    49.86: 36
       49.86 -    62.33: 48
  Dihedral angle restraints: 1932
    sinusoidal: 1032
      harmonic: 900
  Sorted by residual:
  dihedral pdb=" CA  SER D  19 "
           pdb=" C   SER D  19 "
           pdb=" N   GLY D  20 "
           pdb=" CA  GLY D  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.81   26.19     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  SER H  19 "
           pdb=" C   SER H  19 "
           pdb=" N   GLY H  20 "
           pdb=" CA  GLY H  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  SER B  19 "
           pdb=" C   SER B  19 "
           pdb=" N   GLY B  20 "
           pdb=" CA  GLY B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.83   26.17     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 1929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.004 -    0.022: 112
       0.022 -    0.041: 92
       0.041 -    0.059: 27
       0.059 -    0.078: 81
       0.078 -    0.096: 12
  Chirality restraints: 324
  Sorted by residual:
  chirality pdb=" CA  PHE D  23 "
            pdb=" N   PHE D  23 "
            pdb=" C   PHE D  23 "
            pdb=" CB  PHE D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.61   -0.10 2.00e-01 2.50e+01 2.30e-01
  chirality pdb=" CA  PHE H  23 "
            pdb=" N   PHE H  23 "
            pdb=" C   PHE H  23 "
            pdb=" CB  PHE H  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.61   -0.10 2.00e-01 2.50e+01 2.29e-01
  chirality pdb=" CA  PHE I  23 "
            pdb=" N   PHE I  23 "
            pdb=" C   PHE I  23 "
            pdb=" CB  PHE I  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.61   -0.10 2.00e-01 2.50e+01 2.28e-01
  ... (remaining 321 not shown)

  Planarity restraints: 636
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS K  18 "   -0.001 2.00e-02 2.50e+03   6.31e-03 8.96e-01
        pdb=" CG  HIS K  18 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS K  18 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 HIS K  18 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS K  18 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS K  18 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 HIS K  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS K  18 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 HIS K  18 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS L  18 "    0.001 2.00e-02 2.50e+03   6.28e-03 8.88e-01
        pdb=" CG  HIS L  18 "    0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS L  18 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 HIS L  18 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS L  18 "    0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS L  18 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 HIS L  18 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS L  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 HIS L  18 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  18 "   -0.001 2.00e-02 2.50e+03   6.22e-03 8.70e-01
        pdb=" CG  HIS E  18 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  18 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  18 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  18 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  18 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 HIS E  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS E  18 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 HIS E  18 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 633 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.28: 813
        2.28 -     2.84: 8947
        2.84 -     3.39: 9216
        3.39 -     3.95: 13796
        3.95 -     4.50: 18435
  Nonbonded interactions: 51207
  Sorted by model distance:
  nonbonded pdb=" HA  TYC J  37 "
            pdb="HT21 TYC L  37 "
     model   vdw
     1.731 2.270
  nonbonded pdb=" HA  TYC B  37 "
            pdb="HT21 TYC D  37 "
     model   vdw
     1.765 2.270
  nonbonded pdb=" HA  TYC I  37 "
            pdb="HT21 TYC K  37 "
     model   vdw
     1.789 2.270
  nonbonded pdb=" HA  TYC F  37 "
            pdb="HT21 TYC H  37 "
     model   vdw
     1.810 2.270
  nonbonded pdb=" HA  TYC C  37 "
            pdb="HT21 TYC E  37 "
     model   vdw
     1.812 2.270
  ... (remaining 51202 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             2.840
  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:             0.020
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.470
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6279
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      :  0.009   0.035   2076  Z= 0.401
  Angle     :  1.220  11.770   2820  Z= 0.531
  Chirality :  0.045   0.096    324
  Planarity :  0.004   0.008    372
  Dihedral  : 11.935  26.190    684
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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: -4.20 (0.39), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.30), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.004   PHE A  15 
 HIS   0.012   0.007   HIS K  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00906 ( 2076)
  covalent geometry    : angle       1.22009 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   15 PHE cc_start: 0.4850 (t80) cc_final: 0.4619 (m-80)
REVERT: I   16 LEU cc_start: 0.6021 (pt) cc_final: 0.5482 (pt)
REVERT: K   29 SER cc_start: 0.7769 (t) cc_final: 0.7472 (p)
REVERT: K   36 THR cc_start: 0.7643 (t) cc_final: 0.7437 (t)
REVERT: L   36 THR cc_start: 0.7118 (t) cc_final: 0.6914 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0489
  time to fit residues: 4.0148
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  35 ASN
** G  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.143674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.124407 restraints weight = 16943.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.126940 restraints weight = 6715.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.128548 restraints weight = 3571.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.129586 restraints weight = 2251.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4964 r_free = 0.4964 target = 0.130256 restraints weight = 1516.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.4714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2076  Z= 0.135
  Angle     :  0.584   3.702   2820  Z= 0.312
  Chirality :  0.045   0.119    324
  Planarity :  0.002   0.007    372
  Dihedral  :  8.100  19.269    348
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.44 %
    Favored  : 78.70 %
  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: -4.26 (0.40), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.31), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.002   PHE D  15 
 HIS   0.004   0.001   HIS K  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2076)
  covalent geometry    : angle       0.58394 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 0.0497
  time to fit residues: 2.6009
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 ASN
Chi-restraints excluded: chain I residue   21 ASN
Chi-restraints excluded: chain J residue   15 PHE
Chi-restraints excluded: chain K residue   21 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** C  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** 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 = 0.4517 r_free = 0.4517 target = 0.108714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.101168 restraints weight = 20092.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.103515 restraints weight = 6781.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.104995 restraints weight = 3330.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.105873 restraints weight = 2022.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.106525 restraints weight = 1435.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2076  Z= 0.118
  Angle     :  0.538   3.572   2820  Z= 0.291
  Chirality :  0.043   0.121    324
  Planarity :  0.002   0.006    372
  Dihedral  :  6.782  26.550    348
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 23.15 %
    Favored  : 75.46 %
  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: -4.73 (0.33), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.25), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE H  15 
 HIS   0.004   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2076)
  covalent geometry    : angle       0.53837 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 23
  average time/residue: 0.0321
  time to fit residues: 1.1850
Evaluate side-chains
  16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 13
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain J residue   15 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  18 HIS ** 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 = 0.4374 r_free = 0.4374 target = 0.099406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.091707 restraints weight = 21087.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.094039 restraints weight = 7795.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.095454 restraints weight = 3884.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.096390 restraints weight = 2371.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.097004 restraints weight = 1644.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2076  Z= 0.154
  Angle     :  0.539   3.907   2820  Z= 0.299
  Chirality :  0.042   0.113    324
  Planarity :  0.002   0.006    372
  Dihedral  :  6.973  25.744    348
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 26.85 %
    Favored  : 69.91 %
  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: -5.11 (0.31), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.23), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.002   PHE J  23 
 HIS   0.005   0.002   HIS K  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2076)
  covalent geometry    : angle       0.53860 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 13
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 20
  average time/residue: 0.0430
  time to fit residues: 1.3806
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain J residue   15 PHE
Chi-restraints excluded: chain K residue   21 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** E  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  18 HIS ** 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 = 0.4347 r_free = 0.4347 target = 0.098347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.090840 restraints weight = 21536.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.093176 restraints weight = 7803.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.094613 restraints weight = 3836.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.095491 restraints weight = 2287.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.096070 restraints weight = 1567.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2076  Z= 0.131
  Angle     :  0.512   3.773   2820  Z= 0.284
  Chirality :  0.042   0.126    324
  Planarity :  0.002   0.006    372
  Dihedral  :  6.744  26.650    348
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 25.46 %
    Favored  : 71.30 %
  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: -5.15 (0.33), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.25), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.001   PHE J  23 
 HIS   0.006   0.002   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 2076)
  covalent geometry    : angle       0.51158 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 14
  time to evaluate  : 0.096 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0393
  time to fit residues: 1.3022
Evaluate side-chains
  16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 13
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain I residue   21 ASN
Chi-restraints excluded: chain J residue   15 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** G  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  18 HIS ** 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 = 0.4232 r_free = 0.4232 target = 0.091992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.085112 restraints weight = 22306.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.087262 restraints weight = 8404.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.088579 restraints weight = 4167.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.089411 restraints weight = 2507.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.089992 restraints weight = 1710.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.6187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   2076  Z= 0.235
  Angle     :  0.619   3.911   2820  Z= 0.347
  Chirality :  0.044   0.120    324
  Planarity :  0.003   0.009    372
  Dihedral  :  7.575  25.345    348
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 26.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.75 %
    Favored  : 81.25 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 26.39 %
    Favored  : 68.98 %
  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: -5.55 (0.32), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.22 (0.24), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.002   PHE C  23 
 HIS   0.004   0.002   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 2076)
  covalent geometry    : angle       0.61943 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 10
  time to evaluate  : 0.106 
Fit side-chains
REVERT: I   15 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.4222 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 19
  average time/residue: 0.0409
  time to fit residues: 1.2446
Evaluate side-chains
  18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain I residue   15 PHE
Chi-restraints excluded: chain I residue   16 LEU
Chi-restraints excluded: chain I residue   21 ASN
Chi-restraints excluded: chain J residue   15 PHE
Chi-restraints excluded: chain K residue   21 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** I  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  18 HIS ** 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 = 0.4308 r_free = 0.4308 target = 0.096560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.089367 restraints weight = 22225.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.091682 restraints weight = 7998.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.093065 restraints weight = 3891.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.093963 restraints weight = 2343.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.094573 restraints weight = 1566.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.6225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2076  Z= 0.107
  Angle     :  0.494   3.625   2820  Z= 0.277
  Chirality :  0.043   0.127    324
  Planarity :  0.002   0.005    372
  Dihedral  :  6.651  25.729    348
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 27.31 %
    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 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: -5.42 (0.32), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.12 (0.24), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE C  23 
 HIS   0.005   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2076)
  covalent geometry    : angle       0.49379 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.107 
Fit side-chains
REVERT: I   15 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.3684 (m-80)
  outliers start: 5
  outliers final: 4
  residues processed: 17
  average time/residue: 0.0388
  time to fit residues: 1.0353
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain I residue   15 PHE
Chi-restraints excluded: chain I residue   16 LEU
Chi-restraints excluded: chain J residue   15 PHE
Chi-restraints excluded: chain J residue   36 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 6 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** J  18 HIS ** 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 = 0.4327 r_free = 0.4327 target = 0.097489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.090341 restraints weight = 21553.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.092661 restraints weight = 7728.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.094081 restraints weight = 3737.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.094969 restraints weight = 2199.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.095571 restraints weight = 1453.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.6455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2076  Z= 0.105
  Angle     :  0.478   3.594   2820  Z= 0.268
  Chirality :  0.043   0.124    324
  Planarity :  0.002   0.005    372
  Dihedral  :  6.369  24.947    348
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 27.78 %
    Favored  : 70.83 %
  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: -5.36 (0.33), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.25), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE C  23 
 HIS   0.004   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2076)
  covalent geometry    : angle       0.47799 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.079 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 15
  average time/residue: 0.0414
  time to fit residues: 0.9732
Evaluate side-chains
  15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain I residue   16 LEU
Chi-restraints excluded: chain J residue   15 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** J  18 HIS ** 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 = 0.4338 r_free = 0.4338 target = 0.098399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.091199 restraints weight = 21374.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.093550 restraints weight = 7623.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.094978 restraints weight = 3696.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.095866 restraints weight = 2178.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.096475 restraints weight = 1465.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.6586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2076  Z= 0.096
  Angle     :  0.461   3.406   2820  Z= 0.259
  Chirality :  0.042   0.126    324
  Planarity :  0.002   0.005    372
  Dihedral  :  6.119  24.597    348
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 18.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 26.39 %
    Favored  : 71.76 %
  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: -5.34 (0.33), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.25), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE C  23 
 HIS   0.005   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 2076)
  covalent geometry    : angle       0.46109 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.110 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 17
  average time/residue: 0.0408
  time to fit residues: 1.1253
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain I residue   15 PHE
Chi-restraints excluded: chain I residue   16 LEU
Chi-restraints excluded: chain J residue   15 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** J  18 HIS ** 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 = 0.4293 r_free = 0.4293 target = 0.095839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.088796 restraints weight = 21470.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.091015 restraints weight = 7823.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.092398 restraints weight = 3827.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.093311 restraints weight = 2291.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.093858 restraints weight = 1514.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.6725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2076  Z= 0.134
  Angle     :  0.493   2.613   2820  Z= 0.278
  Chirality :  0.042   0.122    324
  Planarity :  0.002   0.005    372
  Dihedral  :  6.351  23.979    348
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 26.85 %
    Favored  : 71.30 %
  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: -5.46 (0.32), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.16 (0.24), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE C  23 
 HIS   0.004   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2076)
  covalent geometry    : angle       0.49312 ( 2820)

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

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

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  480 Ramachandran restraints generated.
    240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 17
  average time/residue: 0.0430
  time to fit residues: 1.1747
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain I residue   15 PHE
Chi-restraints excluded: chain I residue   16 LEU
Chi-restraints excluded: chain J residue   15 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** E  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  18 HIS ** 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 = 0.4344 r_free = 0.4344 target = 0.098760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.091577 restraints weight = 20872.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.093924 restraints weight = 7525.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.095387 restraints weight = 3641.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.096282 restraints weight = 2139.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.096883 restraints weight = 1407.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.6749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2076  Z= 0.085
  Angle     :  0.438   2.750   2820  Z= 0.249
  Chirality :  0.042   0.124    324
  Planarity :  0.001   0.004    372
  Dihedral  :  6.016  24.557    348
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 27.31 %
    Favored  : 71.30 %
  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: -5.35 (0.33), residues: 240
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.07 (0.25), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE C  23 
 HIS   0.005   0.002   HIS H  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 2076)
  covalent geometry    : angle       0.43828 ( 2820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1392.59 seconds
wall clock time: 24 minutes 21.89 seconds (1461.89 seconds total)