Starting phenix.real_space_refine
on Fri Oct 10 10:15:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qn7_18509/10_2025/8qn7_18509.cif"
  }
  resolution = 2.7
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C     920      2.51       5
     N     255      2.21       5
     O     275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1455
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 291
          Classifications: {'peptide': 38}
          Link IDs: {'TRANS': 37}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.31, per 1000 atoms: 0.21
  Number of scatterers: 1455
  At special positions: 0
  Unit cell: (82.584, 72.168, 29.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     275      8.00
     N     255      7.00
     C     920      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: 0.05
  Conformation dependent library (CDL) restraints added in 32.0 milliseconds
  
  Enol-peptide restraints added in 0.0 nanoseconds
  

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  320

  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: 0.28
  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: 0.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 355
        1.33 -     1.45: 410
        1.45 -     1.58: 710
        1.58 -     1.70: 0
        1.70 -     1.82: 10
  Bond restraints: 1485
  Sorted by residual:
  bond pdb=" CA  SER B   8 "
       pdb=" CB  SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.043 1.48e-02 4.57e+03 8.27e+00
  bond pdb=" CA  SER C   8 "
       pdb=" CB  SER C   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.042 1.48e-02 4.57e+03 8.22e+00
  bond pdb=" CA  SER A   8 "
       pdb=" CB  SER A   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.042 1.48e-02 4.57e+03 8.15e+00
  bond pdb=" CA  SER E   8 "
       pdb=" CB  SER E   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.042 1.48e-02 4.57e+03 8.15e+00
  bond pdb=" CA  SER D   8 "
       pdb=" CB  SER D   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.041 1.48e-02 4.57e+03 7.81e+00
  ... (remaining 1480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 1213
        1.08 -     2.17: 553
        2.17 -     3.25: 146
        3.25 -     4.33: 43
        4.33 -     5.42: 30
  Bond angle restraints: 1985
  Sorted by residual:
  angle pdb=" CA  HIS E  13 "
        pdb=" CB  HIS E  13 "
        pdb=" CG  HIS E  13 "
      ideal   model   delta    sigma   weight residual
     113.80  118.98   -5.18 1.00e+00 1.00e+00 2.69e+01
  angle pdb=" CA  HIS A  13 "
        pdb=" CB  HIS A  13 "
        pdb=" CG  HIS A  13 "
      ideal   model   delta    sigma   weight residual
     113.80  118.98   -5.18 1.00e+00 1.00e+00 2.68e+01
  angle pdb=" CA  HIS C  13 "
        pdb=" CB  HIS C  13 "
        pdb=" CG  HIS C  13 "
      ideal   model   delta    sigma   weight residual
     113.80  118.97   -5.17 1.00e+00 1.00e+00 2.68e+01
  angle pdb=" CA  HIS B  13 "
        pdb=" CB  HIS B  13 "
        pdb=" CG  HIS B  13 "
      ideal   model   delta    sigma   weight residual
     113.80  118.97   -5.17 1.00e+00 1.00e+00 2.68e+01
  angle pdb=" CA  HIS D  13 "
        pdb=" CB  HIS D  13 "
        pdb=" CG  HIS D  13 "
      ideal   model   delta    sigma   weight residual
     113.80  118.96   -5.16 1.00e+00 1.00e+00 2.67e+01
  ... (remaining 1980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.04 -    11.62: 709
       11.62 -    23.19: 76
       23.19 -    34.77: 25
       34.77 -    46.35: 15
       46.35 -    57.93: 5
  Dihedral angle restraints: 830
    sinusoidal: 320
      harmonic: 510
  Sorted by residual:
  dihedral pdb=" CA  GLU D  22 "
           pdb=" C   GLU D  22 "
           pdb=" N   ASP D  23 "
           pdb=" CA  ASP D  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.98  -16.02     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  GLU E  22 "
           pdb=" C   GLU E  22 "
           pdb=" N   ASP E  23 "
           pdb=" CA  ASP E  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.01  -15.99     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLU A  22 "
           pdb=" C   GLU A  22 "
           pdb=" N   ASP A  23 "
           pdb=" CA  ASP A  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.01  -15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 827 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 60
       0.042 -    0.082: 54
       0.082 -    0.123: 61
       0.123 -    0.163: 15
       0.163 -    0.204: 10
  Chirality restraints: 200
  Sorted by residual:
  chirality pdb=" CA  HIS B  14 "
            pdb=" N   HIS B  14 "
            pdb=" C   HIS B  14 "
            pdb=" CB  HIS B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  HIS E  14 "
            pdb=" N   HIS E  14 "
            pdb=" C   HIS E  14 "
            pdb=" CB  HIS E  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  HIS D  14 "
            pdb=" N   HIS D  14 "
            pdb=" C   HIS D  14 "
            pdb=" CB  HIS D  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 197 not shown)

  Planarity restraints: 265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E  25 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" C   GLY E  25 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLY E  25 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER E  26 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  25 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   GLY B  25 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLY B  25 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  26 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  25 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   GLY C  25 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLY C  25 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER C  26 "    0.009 2.00e-02 2.50e+03
  ... (remaining 262 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 779
        3.04 -     3.50: 1239
        3.50 -     3.97: 2210
        3.97 -     4.43: 2481
        4.43 -     4.90: 4512
  Nonbonded interactions: 11221
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  16 "
            pdb=" OE1 GLU B  11 "
     model   vdw
     2.570 3.120
  nonbonded pdb=" OE1 GLU A  11 "
            pdb=" NZ  LYS E  16 "
     model   vdw
     2.570 3.120
  nonbonded pdb=" OE1 GLU C  11 "
            pdb=" NZ  LYS D  16 "
     model   vdw
     2.570 3.120
  nonbonded pdb=" N   ALA B  30 "
            pdb=" O   ALA B  30 "
     model   vdw
     2.652 2.496
  nonbonded pdb=" N   ALA C  30 "
            pdb=" O   ALA C  30 "
     model   vdw
     2.653 2.496
  ... (remaining 11216 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.540
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.010
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9066
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      :  0.010   0.043   1485  Z= 0.647
  Angle     :  1.434   5.419   1985  Z= 0.986
  Chirality :  0.087   0.204    200
  Planarity :  0.010   0.058    265
  Dihedral  : 13.541  57.925    510
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  :  0.00 %
    Favored  : 96.55 %
  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 aren not related in a simple way.
  whole: -3.22 (0.33), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.25), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.003   ARG B   5 
 TYR   0.006   0.003   TYR E  10 
 PHE   0.016   0.007   PHE A  19 
 HIS   0.011   0.006   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00966 ( 1485)
  covalent geometry    : angle       1.43395 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.031 
Fit side-chains
REVERT: C    3 GLU cc_start: 0.8908 (tt0) cc_final: 0.8218 (tm-30)
REVERT: E    3 GLU cc_start: 0.8847 (tt0) cc_final: 0.8167 (tm-30)
  outliers start: 5
  outliers final: 0
  residues processed: 52
  average time/residue: 0.3693
  time to fit residues: 19.4271
Evaluate side-chains
  40 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
B  14 HIS
C  14 HIS
E   6 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.137836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.120402 restraints weight = 1523.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.17
r_work: 0.3588 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8977
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   1485  Z= 0.192
  Angle     :  0.622   4.195   1985  Z= 0.327
  Chirality :  0.050   0.111    200
  Planarity :  0.002   0.016    265
  Dihedral  :  5.570  16.503    195
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.52 %
    Favored  : 93.79 %
  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 aren not related in a simple way.
  whole: -3.02 (0.37), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.28), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.004   0.001   TYR A  10 
 PHE   0.008   0.002   PHE D  19 
 HIS   0.007   0.003   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 1485)
  covalent geometry    : angle       0.62184 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.037 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8404 (tt0) cc_final: 0.8159 (mt-10)
REVERT: B    3 GLU cc_start: 0.8624 (tt0) cc_final: 0.8306 (mt-10)
REVERT: D    3 GLU cc_start: 0.8362 (tt0) cc_final: 0.7951 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4651
  time to fit residues: 20.6760
Evaluate side-chains
  44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 3 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.140099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.123192 restraints weight = 1562.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.19
r_work: 0.3632 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8957
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   1485  Z= 0.107
  Angle     :  0.459   3.146   1985  Z= 0.245
  Chirality :  0.049   0.118    200
  Planarity :  0.001   0.009    265
  Dihedral  :  5.103  15.555    195
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.34 %
    Favored  : 88.97 %
  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 aren not related in a simple way.
  whole: -3.07 (0.38), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.29), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   5 
 TYR   0.007   0.001   TYR C  10 
 PHE   0.005   0.001   PHE A  19 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 1485)
  covalent geometry    : angle       0.45893 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8349 (tt0) cc_final: 0.8127 (mt-10)
REVERT: D    3 GLU cc_start: 0.8374 (tt0) cc_final: 0.7955 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 42
  average time/residue: 0.7981
  time to fit residues: 33.8863
Evaluate side-chains
  41 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.6188

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.137896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.120574 restraints weight = 1570.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.21
r_work: 0.3594 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   1485  Z= 0.147
  Angle     :  0.499   3.426   1985  Z= 0.264
  Chirality :  0.050   0.117    200
  Planarity :  0.002   0.012    265
  Dihedral  :  5.153  15.791    195
  Min Nonbonded Distance : 2.690

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 13.10 %
    Favored  : 86.21 %
  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 aren not related in a simple way.
  whole: -3.06 (0.40), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.007   0.001   PHE A  19 
 HIS   0.005   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 1485)
  covalent geometry    : angle       0.49860 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8387 (tt0) cc_final: 0.8098 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 43
  average time/residue: 0.7870
  time to fit residues: 34.1971
Evaluate side-chains
  43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.138786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.121700 restraints weight = 1581.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.20
r_work: 0.3621 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8966
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   1485  Z= 0.112
  Angle     :  0.444   3.070   1985  Z= 0.237
  Chirality :  0.049   0.118    200
  Planarity :  0.001   0.009    265
  Dihedral  :  4.933  15.457    195
  Min Nonbonded Distance : 2.688

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.41 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.05 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.006   0.001   PHE A  19 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 1485)
  covalent geometry    : angle       0.44384 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8403 (tt0) cc_final: 0.8115 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 46
  average time/residue: 0.7974
  time to fit residues: 37.0530
Evaluate side-chains
  42 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.136929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119640 restraints weight = 1543.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.18
r_work: 0.3590 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   1485  Z= 0.142
  Angle     :  0.487   3.342   1985  Z= 0.259
  Chirality :  0.049   0.118    200
  Planarity :  0.002   0.013    265
  Dihedral  :  5.032  15.541    195
  Min Nonbonded Distance : 2.687

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.41 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.11 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.32), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.007   0.001   PHE A  19 
 HIS   0.004   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 1485)
  covalent geometry    : angle       0.48735 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8438 (tt0) cc_final: 0.8079 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 46
  average time/residue: 0.8157
  time to fit residues: 37.8942
Evaluate side-chains
  43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.135295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117842 restraints weight = 1560.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.19
r_work: 0.3570 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   1485  Z= 0.197
  Angle     :  0.553   3.883   1985  Z= 0.291
  Chirality :  0.050   0.117    200
  Planarity :  0.002   0.014    265
  Dihedral  :  5.219  16.291    195
  Min Nonbonded Distance : 2.686

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.72 %
    Favored  : 84.83 %
  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 aren not related in a simple way.
  whole: -3.23 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.005   0.001   TYR B  10 
 PHE   0.009   0.001   PHE A  19 
 HIS   0.005   0.002   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 1485)
  covalent geometry    : angle       0.55250 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 47
  average time/residue: 0.8078
  time to fit residues: 38.3385
Evaluate side-chains
  43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.135206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.117448 restraints weight = 1547.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.18
r_work: 0.3562 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   1485  Z= 0.195
  Angle     :  0.553   3.830   1985  Z= 0.291
  Chirality :  0.050   0.116    200
  Planarity :  0.002   0.019    265
  Dihedral  :  5.195  16.488    195
  Min Nonbonded Distance : 2.685

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.41 %
    Favored  : 84.83 %
  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 aren not related in a simple way.
  whole: -3.27 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.009   0.001   PHE D  19 
 HIS   0.005   0.002   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 1485)
  covalent geometry    : angle       0.55334 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 46
  average time/residue: 0.7479
  time to fit residues: 34.7393
Evaluate side-chains
  43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0870
   chunk 11 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.2166

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.140748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.123684 restraints weight = 1526.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.16
r_work: 0.3654 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.007   1485  Z= 0.081
  Angle     :  0.401   2.906   1985  Z= 0.218
  Chirality :  0.049   0.120    200
  Planarity :  0.001   0.006    265
  Dihedral  :  4.640  15.041    195
  Min Nonbonded Distance : 2.686

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  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 aren not related in a simple way.
  whole: -3.20 (0.42), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.32), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.004   0.001   PHE D  19 
 HIS   0.002   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 ( 1485)
  covalent geometry    : angle       0.40143 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.038 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.7198
  time to fit residues: 29.8120
Evaluate side-chains
  41 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.134526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.117023 restraints weight = 1536.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.17
r_work: 0.3557 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.020   1485  Z= 0.226
  Angle     :  0.584   3.968   1985  Z= 0.308
  Chirality :  0.050   0.117    200
  Planarity :  0.002   0.019    265
  Dihedral  :  5.177  16.267    195
  Min Nonbonded Distance : 2.682

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.10 %
    Favored  : 84.83 %
  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 aren not related in a simple way.
  whole: -3.33 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.011   0.002   PHE A  19 
 HIS   0.005   0.002   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 1485)
  covalent geometry    : angle       0.58388 ( 1985)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.036 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 45
  average time/residue: 0.6807
  time to fit residues: 30.9160
Evaluate side-chains
  46 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   22 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.135229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117715 restraints weight = 1516.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.17
r_work: 0.3565 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.019   1485  Z= 0.205
  Angle     :  0.570   3.866   1985  Z= 0.300
  Chirality :  0.050   0.117    200
  Planarity :  0.002   0.018    265
  Dihedral  :  5.203  16.503    195
  Min Nonbonded Distance : 2.683

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.79 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.36 (0.41), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.31), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.006   0.001   TYR E  10 
 PHE   0.009   0.001   PHE A  19 
 HIS   0.005   0.002   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 1485)
  covalent geometry    : angle       0.56978 ( 1985)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 985.07 seconds
wall clock time: 18 minutes 11.97 seconds (1091.97 seconds total)