Starting phenix.real_space_refine
on Wed Sep 17 03:11:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9luo_63400/09_2025/9luo_63400.cif"
  }
  resolution = 3.07
  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=   0.005
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      13      5.16       5
     C    1617      2.51       5
     N     436      2.21       5
     O     474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2540
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 534
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 534
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 907
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
    Chain: "D"
      Number of atoms: 1099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1099
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
          Chain breaks: 2
  Time building chain proxies: 1.07, per 1000 atoms: 0.42
  Number of scatterers: 2540
  At special positions: 0
  Unit cell: (62.5884, 82.7061, 87.1767, 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      13     16.00
     O     474      8.00
     N     436      7.00
     C    1617      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: 0.22
  Conformation dependent library (CDL) restraints added in 103.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  604

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      79.9% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 300 through 316
      removed outlier: 3.560A  pdb=" N   ALA A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 334
      removed outlier: 4.066A  pdb=" N   LEU A 334 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 4.087A  pdb=" N   LEU A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   MET A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLN A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 383
    Processing helix  chain 'A' and resid 537 through 547
    Processing helix  chain 'C' and resid 31 through 35
      removed outlier: 3.649A  pdb=" N   LEU C  35 " --> pdb=" O   PHE C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 45
    Processing helix  chain 'C' and resid 48 through 56
    Processing helix  chain 'C' and resid 59 through 67
    Processing helix  chain 'C' and resid 68 through 79
      removed outlier: 3.707A  pdb=" N   TRP C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   HIS C  79 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 97
    Processing helix  chain 'C' and resid 99 through 107
      removed outlier: 3.574A  pdb=" N   LEU C 103 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   TYR C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 113
    Processing helix  chain 'C' and resid 122 through 141
      removed outlier: 3.555A  pdb=" N   SER C 130 " --> pdb=" O   LYS C 126 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   SER C 141 " --> pdb=" O   TYR C 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 25
    Processing helix  chain 'D' and resid 27 through 33
    Processing helix  chain 'D' and resid 49 through 68
    Processing helix  chain 'D' and resid 89 through 103
      removed outlier: 3.632A  pdb=" N   LYS D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 120
    Processing helix  chain 'D' and resid 121 through 137
    Processing helix  chain 'D' and resid 140 through 148
      removed outlier: 3.740A  pdb=" N   ILE D 144 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE D 148 " --> pdb=" O   ILE D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 166
      removed outlier: 3.517A  pdb=" N   ASN D 166 " --> pdb=" O   VAL D 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 10

    155 hydrogen bonds defined for protein.
    456 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.34

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.04 -     1.19: 1
        1.19 -     1.35: 828
        1.35 -     1.50: 660
        1.50 -     1.66: 1076
        1.66 -     1.81: 20
  Bond restraints: 2585
  Sorted by residual:
  bond pdb=" CG  PRO C 114 "
       pdb=" CD  PRO C 114 "
    ideal  model  delta    sigma   weight residual
    1.503  1.041  0.462 3.40e-02 8.65e+02 1.85e+02
  bond pdb=" N   PRO C 114 "
       pdb=" CA  PRO C 114 "
    ideal  model  delta    sigma   weight residual
    1.468  1.522 -0.053 1.10e-02 8.26e+03 2.37e+01
  bond pdb=" CB  PRO C 114 "
       pdb=" CG  PRO C 114 "
    ideal  model  delta    sigma   weight residual
    1.492  1.344  0.148 5.00e-02 4.00e+02 8.74e+00
  bond pdb=" CA  PRO C 114 "
       pdb=" CB  PRO C 114 "
    ideal  model  delta    sigma   weight residual
    1.536  1.490  0.045 1.69e-02 3.50e+03 7.23e+00
  bond pdb=" N   PRO C 114 "
       pdb=" CD  PRO C 114 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 5.80e+00
  ... (remaining 2580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.64: 3475
        6.64 -    13.29: 3
       13.29 -    19.93: 0
       19.93 -    26.58: 1
       26.58 -    33.22: 2
  Bond angle restraints: 3481
  Sorted by residual:
  angle pdb=" N   PRO C 114 "
        pdb=" CD  PRO C 114 "
        pdb=" CG  PRO C 114 "
      ideal   model   delta    sigma   weight residual
     103.20   72.32   30.88 1.50e+00 4.44e-01 4.24e+02
  angle pdb=" CA  PRO C 114 "
        pdb=" CB  PRO C 114 "
        pdb=" CG  PRO C 114 "
      ideal   model   delta    sigma   weight residual
     104.50   71.28   33.22 1.90e+00 2.77e-01 3.06e+02
  angle pdb=" CB  PRO C 114 "
        pdb=" CG  PRO C 114 "
        pdb=" CD  PRO C 114 "
      ideal   model   delta    sigma   weight residual
     106.10  127.68  -21.58 3.20e+00 9.77e-02 4.55e+01
  angle pdb=" CA  PRO C 114 "
        pdb=" N   PRO C 114 "
        pdb=" CD  PRO C 114 "
      ideal   model   delta    sigma   weight residual
     112.00  104.08    7.92 1.40e+00 5.10e-01 3.20e+01
  angle pdb=" N   PRO C 114 "
        pdb=" CA  PRO C 114 "
        pdb=" CB  PRO C 114 "
      ideal   model   delta    sigma   weight residual
     102.33   95.83    6.50 1.18e+00 7.18e-01 3.04e+01
  ... (remaining 3476 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 1333
       17.99 -    35.98: 172
       35.98 -    53.97: 39
       53.97 -    71.96: 17
       71.96 -    89.95: 1
  Dihedral angle restraints: 1562
    sinusoidal: 641
      harmonic: 921
  Sorted by residual:
  dihedral pdb=" N   PRO C 114 "
           pdb=" CG  PRO C 114 "
           pdb=" CD  PRO C 114 "
           pdb=" CB  PRO C 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.81   56.81     1      1.50e+01 4.44e-03 1.93e+01
  dihedral pdb=" CA  PRO C 114 "
           pdb=" CB  PRO C 114 "
           pdb=" CG  PRO C 114 "
           pdb=" CD  PRO C 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -38.00 -109.46   71.46     1      2.00e+01 2.50e-03 1.64e+01
  dihedral pdb=" CA  ILE C  83 "
           pdb=" C   ILE C  83 "
           pdb=" N   GLY C  84 "
           pdb=" CA  GLY C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 266
       0.027 -    0.055: 84
       0.055 -    0.082: 22
       0.082 -    0.109: 16
       0.109 -    0.136: 4
  Chirality restraints: 392
  Sorted by residual:
  chirality pdb=" CA  ILE D  19 "
            pdb=" N   ILE D  19 "
            pdb=" C   ILE D  19 "
            pdb=" CB  ILE D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  PRO D 141 "
            pdb=" N   PRO D 141 "
            pdb=" C   PRO D 141 "
            pdb=" CB  PRO D 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  THR C  81 "
            pdb=" N   THR C  81 "
            pdb=" C   THR C  81 "
            pdb=" CB  THR C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.31e-01
  ... (remaining 389 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 336 "   -0.034 5.00e-02 4.00e+02   5.06e-02 4.10e+00
        pdb=" N   PRO A 337 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 140 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO D 141 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 141 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 141 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  43 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO D  44 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO D  44 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D  44 "    0.025 5.00e-02 4.00e+02
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 214
        2.74 -     3.28: 2497
        3.28 -     3.82: 4161
        3.82 -     4.36: 4550
        4.36 -     4.90: 8131
  Nonbonded interactions: 19553
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 105 "
            pdb=" OG1 THR D 108 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PHE A 540 "
            pdb=" OG  SER A 544 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NE2 GLN A 311 "
            pdb=" OE1 GLN A 542 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OD1 ASP C  48 "
            pdb=" OG1 THR C  51 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NE2 HIS C  63 "
            pdb=" OE1 GLN C  67 "
     model   vdw
     2.376 3.120
  ... (remaining 19548 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.230
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.120
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
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   0.462   2585  Z= 0.317
  Angle     :  1.050  33.222   3481  Z= 0.571
  Chirality :  0.035   0.136    392
  Planarity :  0.005   0.051    438
  Dihedral  : 17.374  89.954    958
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.22 %
    Favored  : 79.78 %
  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:  1.57 (0.51), residues: 302
  helix:  1.64 (0.35), residues: 231
  sheet:  None (None), residues: 0
  loop : -0.89 (0.83), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 163 
 TYR   0.003   0.000   TYR D 118 
 PHE   0.008   0.001   PHE D 110 
 TRP   0.014   0.002   TRP D 168 
 HIS   0.002   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00995 ( 2585)
  covalent geometry    : angle       1.04955 ( 3481)
  hydrogen bonds       : bond        0.14622 (  155)
  hydrogen bonds       : angle       4.96339 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: C  114 PRO cc_start: 0.6337 (Cg_endo) cc_final: 0.6075 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0804
  time to fit residues: 4.5256
Evaluate side-chains
  45 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0040
   chunk 15 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.202071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.167893 restraints weight = 3162.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.15
r_work: 0.3943 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2585  Z= 0.132
  Angle     :  0.626  12.383   3481  Z= 0.306
  Chirality :  0.037   0.123    392
  Planarity :  0.005   0.052    438
  Dihedral  :  3.977  17.146    330
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.41 %
    Favored  : 78.34 %
  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:  1.63 (0.50), residues: 302
  helix:  1.58 (0.34), residues: 233
  sheet:  None (None), residues: 0
  loop : -0.52 (0.85), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 163 
 TYR   0.005   0.001   TYR C 136 
 PHE   0.007   0.001   PHE D 110 
 TRP   0.007   0.001   TRP A 336 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2585)
  covalent geometry    : angle       0.62596 ( 3481)
  hydrogen bonds       : bond        0.03819 (  155)
  hydrogen bonds       : angle       3.88531 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: C  114 PRO cc_start: 0.6410 (OUTLIER) cc_final: 0.6157 (Cg_endo)
  outliers start: 9
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0586
  time to fit residues: 3.5426
Evaluate side-chains
  50 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  114 PRO
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 311 GLN
A 542 GLN
C  67 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.201041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.166737 restraints weight = 3198.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 2.17
r_work: 0.3926 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2585  Z= 0.133
  Angle     :  0.615  12.415   3481  Z= 0.299
  Chirality :  0.037   0.125    392
  Planarity :  0.005   0.052    438
  Dihedral  :  4.120  17.649    330
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 19.13 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.51), residues: 302
  helix:  1.64 (0.35), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.29 (0.88), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 163 
 TYR   0.005   0.001   TYR A 301 
 PHE   0.008   0.001   PHE C 120 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2585)
  covalent geometry    : angle       0.61548 ( 3481)
  hydrogen bonds       : bond        0.03776 (  155)
  hydrogen bonds       : angle       3.81732 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6967 (tt)
REVERT: C  114 PRO cc_start: 0.6550 (Cg_endo) cc_final: 0.6326 (Cg_endo)
  outliers start: 14
  outliers final: 9
  residues processed: 56
  average time/residue: 0.0556
  time to fit residues: 3.8170
Evaluate side-chains
  54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  151 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
C  67 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.201525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.167760 restraints weight = 3210.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.15
r_work: 0.3931 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2585  Z= 0.115
  Angle     :  0.561  10.172   3481  Z= 0.273
  Chirality :  0.037   0.133    392
  Planarity :  0.004   0.052    438
  Dihedral  :  3.990  15.664    330
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.13 %
    Favored  : 77.26 %
  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:  1.90 (0.51), residues: 302
  helix:  1.74 (0.35), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.34 (0.88), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 163 
 TYR   0.004   0.001   TYR C 137 
 PHE   0.006   0.001   PHE C 120 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.002   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 2585)
  covalent geometry    : angle       0.56149 ( 3481)
  hydrogen bonds       : bond        0.03362 (  155)
  hydrogen bonds       : angle       3.73472 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0520
  time to fit residues: 3.1618
Evaluate side-chains
  53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0670
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
C  67 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.201944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.168079 restraints weight = 3218.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 2.17
r_work: 0.3930 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2585  Z= 0.115
  Angle     :  0.541  10.741   3481  Z= 0.264
  Chirality :  0.037   0.132    392
  Planarity :  0.004   0.052    438
  Dihedral  :  3.983  15.808    330
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.86 %
    Favored  : 76.17 %
  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:  1.90 (0.51), residues: 302
  helix:  1.76 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.39 (0.87), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 163 
 TYR   0.004   0.001   TYR C 137 
 PHE   0.007   0.001   PHE C 120 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.002   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2585)
  covalent geometry    : angle       0.54058 ( 3481)
  hydrogen bonds       : bond        0.03345 (  155)
  hydrogen bonds       : angle       3.68346 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6940 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0493
  time to fit residues: 3.1464
Evaluate side-chains
  54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0670
   chunk 15 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
C  67 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.202646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.168964 restraints weight = 3160.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.14
r_work: 0.3942 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2585  Z= 0.107
  Angle     :  0.523  10.592   3481  Z= 0.257
  Chirality :  0.036   0.131    392
  Planarity :  0.004   0.051    438
  Dihedral  :  3.872  15.240    330
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.22 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.51), residues: 302
  helix:  1.83 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.41 (0.87), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 163 
 TYR   0.004   0.001   TYR C 137 
 PHE   0.006   0.001   PHE D 154 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.002   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2585)
  covalent geometry    : angle       0.52312 ( 3481)
  hydrogen bonds       : bond        0.03100 (  155)
  hydrogen bonds       : angle       3.62793 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6925 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0547
  time to fit residues: 3.4394
Evaluate side-chains
  52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0980
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C  67 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.202076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.168242 restraints weight = 3177.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.15
r_work: 0.3940 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2585  Z= 0.113
  Angle     :  0.546  11.403   3481  Z= 0.265
  Chirality :  0.037   0.129    392
  Planarity :  0.004   0.051    438
  Dihedral  :  3.904  15.187    330
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.22 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.51), residues: 302
  helix:  1.78 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.42 (0.87), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 163 
 TYR   0.005   0.001   TYR C 136 
 PHE   0.006   0.001   PHE A 304 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.002   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2585)
  covalent geometry    : angle       0.54573 ( 3481)
  hydrogen bonds       : bond        0.03185 (  155)
  hydrogen bonds       : angle       3.65362 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6937 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0573
  time to fit residues: 3.5627
Evaluate side-chains
  52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.4357 r_free = 0.4357 target = 0.201156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.167280 restraints weight = 3202.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 2.16
r_work: 0.3935 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2585  Z= 0.124
  Angle     :  0.561  11.734   3481  Z= 0.272
  Chirality :  0.037   0.128    392
  Planarity :  0.004   0.051    438
  Dihedral  :  3.926  14.473    330
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.66 %
    Favored  : 75.09 %
  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:  1.83 (0.51), residues: 302
  helix:  1.71 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.45 (0.88), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 163 
 TYR   0.004   0.001   TYR A 301 
 PHE   0.007   0.001   PHE A 304 
 TRP   0.007   0.001   TRP A 336 
 HIS   0.003   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2585)
  covalent geometry    : angle       0.56066 ( 3481)
  hydrogen bonds       : bond        0.03369 (  155)
  hydrogen bonds       : angle       3.71695 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6955 (tt)
REVERT: D  167 GLN cc_start: 0.7216 (tp40) cc_final: 0.6172 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0523
  time to fit residues: 3.4795
Evaluate side-chains
  50 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  140 MET
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 15 optimal weight:    0.0870
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.3698

-------------------------------------------------------------------------------
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 = 0.4382 r_free = 0.4382 target = 0.202943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.169097 restraints weight = 3240.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 2.20
r_work: 0.3952 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2585  Z= 0.102
  Angle     :  0.542  11.927   3481  Z= 0.263
  Chirality :  0.036   0.133    392
  Planarity :  0.004   0.051    438
  Dihedral  :  3.820  15.133    330
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.38 %
    Favored  : 75.45 %
  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:  1.95 (0.51), residues: 302
  helix:  1.80 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.43 (0.88), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 163 
 TYR   0.004   0.001   TYR C  41 
 PHE   0.010   0.001   PHE D 170 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2585)
  covalent geometry    : angle       0.54171 ( 3481)
  hydrogen bonds       : bond        0.02930 (  155)
  hydrogen bonds       : angle       3.65492 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6921 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0587
  time to fit residues: 3.5158
Evaluate side-chains
  49 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  143 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.195384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.161491 restraints weight = 3249.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.12
r_work: 0.3864 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   2585  Z= 0.212
  Angle     :  0.700  12.939   3481  Z= 0.344
  Chirality :  0.042   0.156    392
  Planarity :  0.004   0.050    438
  Dihedral  :  4.239  15.902    330
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.02 %
    Favored  : 75.45 %
  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:  1.17 (0.50), residues: 302
  helix:  1.25 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.70 (0.87), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.008   0.002   TYR A 301 
 PHE   0.009   0.002   PHE D 154 
 TRP   0.013   0.002   TRP C 109 
 HIS   0.006   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 2585)
  covalent geometry    : angle       0.69964 ( 3481)
  hydrogen bonds       : bond        0.04535 (  155)
  hydrogen bonds       : angle       4.06066 (  456)

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7017 (tt)
  outliers start: 7
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0571
  time to fit residues: 3.6000
Evaluate side-chains
  51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain D residue   11 SER
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  128 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4333 r_free = 0.4333 target = 0.198064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.164519 restraints weight = 3227.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.12
r_work: 0.3856 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2585  Z= 0.129
  Angle     :  0.609  13.068   3481  Z= 0.297
  Chirality :  0.038   0.133    392
  Planarity :  0.004   0.049    438
  Dihedral  :  4.043  15.015    330
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.38 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.51), residues: 302
  helix:  1.53 (0.34), residues: 234
  sheet:  None (None), residues: 0
  loop : -0.59 (0.88), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 163 
 TYR   0.004   0.001   TYR A 301 
 PHE   0.009   0.001   PHE D 170 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2585)
  covalent geometry    : angle       0.60869 ( 3481)
  hydrogen bonds       : bond        0.03487 (  155)
  hydrogen bonds       : angle       3.85237 (  456)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 955.11 seconds
wall clock time: 17 minutes 5.10 seconds (1025.10 seconds total)