Starting phenix.real_space_refine
on Wed Sep 17 02:57:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9as3_43803/09_2025/9as3_43803.map"
  }
  resolution = 3.18
  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=   0.018
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      15      5.16       5
     C    1278      2.51       5
     N     286      2.21       5
     O     311      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 1890
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1866
          Classifications: {'peptide': 245}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 8, 'TRANS': 236}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'7LD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.50, per 1000 atoms: 0.26
  Number of scatterers: 1890
  At special positions: 0
  Unit cell: (59.84, 70.4, 67.76, 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      15     16.00
     O     311      8.00
     N     286      7.00
     C    1278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 148 " - pdb=" SG  CYS A 227 " distance=2.03

  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: 0.16
  Conformation dependent library (CDL) restraints added in 51.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  470

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 0 sheets defined
      82.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 99
      removed outlier: 3.639A  pdb=" N   LEU A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET A  97 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA A  98 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 122
      removed outlier: 3.805A  pdb=" N   LEU A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 137
    Processing helix  chain 'A' and resid 147 through 179
    Processing helix  chain 'A' and resid 179 through 186
      removed outlier: 3.824A  pdb=" N   PHE A 186 " --> pdb=" O   HIS A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 207
      removed outlier: 3.753A  pdb=" N   SER A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   SER A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.642A  pdb=" N   VAL A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.524A  pdb=" N   ILE A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 261
    Processing helix  chain 'A' and resid 316 through 347
      Proline residue:  A 338  - end of helix
      removed outlier: 3.863A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 382
      removed outlier: 3.775A  pdb=" N   TRP A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 370 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
      removed outlier: 3.512A  pdb=" N   THR A 381 " --> pdb=" O   PRO A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 393

    132 hydrogen bonds defined for protein.
    396 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: 0.14

  Time building geometry restraints manager: 0.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 537
        1.35 -     1.46: 506
        1.46 -     1.58: 868
        1.58 -     1.70: 0
        1.70 -     1.82: 25
  Bond restraints: 1936
  Sorted by residual:
  bond pdb=" CA  SER A 188 "
       pdb=" CB  SER A 188 "
    ideal  model  delta    sigma   weight residual
    1.528  1.492  0.036 1.34e-02 5.57e+03 7.31e+00
  bond pdb=" N   ASN A 384 "
       pdb=" CA  ASN A 384 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.29e-02 6.01e+03 6.72e+00
  bond pdb=" N   ASN A 107 "
       pdb=" CA  ASN A 107 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.63e+00
  bond pdb=" N   SER A 188 "
       pdb=" CA  SER A 188 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.19e-02 7.06e+03 6.15e+00
  bond pdb=" N   TYR A 370 "
       pdb=" CA  TYR A 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.71e+00
  ... (remaining 1931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 2384
        1.24 -     2.48: 199
        2.48 -     3.73: 39
        3.73 -     4.97: 15
        4.97 -     6.21: 8
  Bond angle restraints: 2645
  Sorted by residual:
  angle pdb=" CA  PRO A 377 "
        pdb=" N   PRO A 377 "
        pdb=" CD  PRO A 377 "
      ideal   model   delta    sigma   weight residual
     112.00  105.79    6.21 1.40e+00 5.10e-01 1.97e+01
  angle pdb=" N   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" C   PHE A 222 "
      ideal   model   delta    sigma   weight residual
     107.73  112.27   -4.54 1.34e+00 5.57e-01 1.15e+01
  angle pdb=" CA  ASN A 107 "
        pdb=" C   ASN A 107 "
        pdb=" O   ASN A 107 "
      ideal   model   delta    sigma   weight residual
     121.81  118.91    2.90 1.18e+00 7.18e-01 6.05e+00
  angle pdb=" CA  SER A 188 "
        pdb=" C   SER A 188 "
        pdb=" O   SER A 188 "
      ideal   model   delta    sigma   weight residual
     120.65  117.65    3.00 1.23e+00 6.61e-01 5.95e+00
  angle pdb=" CA  SER A 203 "
        pdb=" C   SER A 203 "
        pdb=" O   SER A 203 "
      ideal   model   delta    sigma   weight residual
     120.82  118.31    2.51 1.05e+00 9.07e-01 5.71e+00
  ... (remaining 2640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 1093
       34.50 -    68.99: 29
       68.99 -   103.49: 5
      103.49 -   137.98: 0
      137.98 -   172.48: 1
  Dihedral angle restraints: 1128
    sinusoidal: 409
      harmonic: 719
  Sorted by residual:
  dihedral pdb=" CA  LYS A 223 "
           pdb=" C   LYS A 223 "
           pdb=" N   GLU A 224 "
           pdb=" CA  GLU A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.79   24.21     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" C16 7LD A 501 "
           pdb=" C17 7LD A 501 "
           pdb=" N3  7LD A 501 "
           pdb=" C18 7LD A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.75  -95.77 -172.48     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CA  GLU A 224 "
           pdb=" C   GLU A 224 "
           pdb=" N   GLY A 225 "
           pdb=" CA  GLY A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.50  -19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 1125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 260
       0.052 -    0.103: 62
       0.103 -    0.155: 7
       0.155 -    0.207: 1
       0.207 -    0.259: 1
  Chirality restraints: 331
  Sorted by residual:
  chirality pdb=" C11 7LD A 501 "
            pdb=" C15 7LD A 501 "
            pdb=" C9  7LD A 501 "
            pdb=" N2  7LD A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.22    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  SER A 188 "
            pdb=" N   SER A 188 "
            pdb=" C   SER A 188 "
            pdb=" CB  SER A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CA  VAL A 221 "
            pdb=" N   VAL A 221 "
            pdb=" C   VAL A 221 "
            pdb=" CB  VAL A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 328 not shown)

  Planarity restraints: 307
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 376 "    0.074 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO A 377 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO A 377 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 377 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 245 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO A 246 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 141 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 142 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 142 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 142 "    0.035 5.00e-02 4.00e+02
  ... (remaining 304 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 487
        2.80 -     3.32: 1812
        3.32 -     3.85: 3012
        3.85 -     4.37: 3511
        4.37 -     4.90: 5981
  Nonbonded interactions: 14803
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 377 "
            pdb=" OG1 THR A 381 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA A 161 "
            pdb=" ND1 HIS A 165 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" OD1 ASP A 155 "
            pdb=" N2  7LD A 501 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" OE1 GLN A 106 "
            pdb=" OH  TYR A 111 "
     model   vdw
     2.446 3.040
  nonbonded pdb=" OD2 ASP A 155 "
            pdb=" OH  TYR A 370 "
     model   vdw
     2.456 3.040
  ... (remaining 14798 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.600
  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:                     2.550
  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:0.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
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      :  0.006   0.060   1937  Z= 0.277
  Angle     :  0.859   6.212   2647  Z= 0.470
  Chirality :  0.044   0.259    331
  Planarity :  0.009   0.108    307
  Dihedral  : 18.431 172.476    655
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 19.10 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.31 (0.52), residues: 235
  helix: -1.22 (0.35), residues: 194
  sheet:  None (None), residues: 0
  loop : -2.10 (1.02), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.011   0.002   TYR A 153 
 PHE   0.007   0.001   PHE A 365 
 TRP   0.005   0.001   TRP A 151 
 HIS   0.004   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 1936)
  covalent geometry    : angle       0.85941 ( 2645)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       0.27407 (    2)
  hydrogen bonds       : bond        0.27550 (  132)
  hydrogen bonds       : angle       8.56600 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.036 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0327
  time to fit residues: 1.4133
Evaluate side-chains
  33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0870
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0470
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.153170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137706 restraints weight = 2408.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.49
r_work: 0.3458 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1937  Z= 0.136
  Angle     :  0.546   4.875   2647  Z= 0.296
  Chirality :  0.040   0.127    331
  Planarity :  0.007   0.057    307
  Dihedral  : 13.575 175.557    275
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 20.60 %
    Favored  : 78.39 %
  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:  0.07 (0.56), residues: 235
  helix:  0.62 (0.37), residues: 203
  sheet:  None (None), residues: 0
  loop : -3.35 (0.99), residues: 32

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 388 
 TYR   0.008   0.001   TYR A 370 
 PHE   0.009   0.001   PHE A 339 
 TRP   0.007   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 1936)
  covalent geometry    : angle       0.54569 ( 2645)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.48537 (    2)
  hydrogen bonds       : bond        0.04673 (  132)
  hydrogen bonds       : angle       4.43733 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.037 
Fit side-chains
REVERT: A  237 ILE cc_start: 0.7940 (tt) cc_final: 0.7691 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0275
  time to fit residues: 1.1183
Evaluate side-chains
  30 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133731 restraints weight = 2455.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.45
r_work: 0.3384 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1937  Z= 0.143
  Angle     :  0.546   5.016   2647  Z= 0.290
  Chirality :  0.041   0.127    331
  Planarity :  0.006   0.049    307
  Dihedral  : 13.121 168.268    275
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.10 %
    Favored  : 77.89 %
  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:  0.76 (0.57), residues: 235
  helix:  1.15 (0.38), residues: 203
  sheet:  None (None), residues: 0
  loop : -3.63 (0.86), residues: 32

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 388 
 TYR   0.006   0.001   TYR A 370 
 PHE   0.009   0.001   PHE A 339 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 1936)
  covalent geometry    : angle       0.54579 ( 2645)
  SS BOND              : bond        0.00251 (    1)
  SS BOND              : angle       0.28138 (    2)
  hydrogen bonds       : bond        0.04178 (  132)
  hydrogen bonds       : angle       3.96215 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.039 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7893 (tmm) cc_final: 0.7610 (tpp)
REVERT: A  237 ILE cc_start: 0.7819 (tt) cc_final: 0.7534 (tt)
REVERT: A  343 ASN cc_start: 0.8003 (t0) cc_final: 0.7695 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0272
  time to fit residues: 1.1171
Evaluate side-chains
  30 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.145080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130198 restraints weight = 2424.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.36
r_work: 0.3384 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1937  Z= 0.146
  Angle     :  0.552   5.443   2647  Z= 0.291
  Chirality :  0.041   0.160    331
  Planarity :  0.005   0.049    307
  Dihedral  : 12.591 155.883    275
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.60 %
    Favored  : 76.88 %
  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:  0.94 (0.57), residues: 235
  helix:  1.31 (0.38), residues: 203
  sheet:  None (None), residues: 0
  loop : -3.83 (0.77), residues: 32

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.006   0.001   TYR A 370 
 PHE   0.009   0.001   PHE A 339 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 1936)
  covalent geometry    : angle       0.55217 ( 2645)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       0.25708 (    2)
  hydrogen bonds       : bond        0.04042 (  132)
  hydrogen bonds       : angle       3.87108 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7944 (tmm) cc_final: 0.7646 (tpp)
REVERT: A  237 ILE cc_start: 0.7869 (tt) cc_final: 0.7590 (tt)
REVERT: A  343 ASN cc_start: 0.7994 (t0) cc_final: 0.7705 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.0455
  time to fit residues: 2.0226
Evaluate side-chains
  35 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 17 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.145574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130710 restraints weight = 2427.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.36
r_work: 0.3397 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1937  Z= 0.135
  Angle     :  0.543   6.232   2647  Z= 0.283
  Chirality :  0.041   0.169    331
  Planarity :  0.005   0.050    307
  Dihedral  : 11.692 136.609    275
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.60 %
    Favored  : 76.88 %
  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:  1.08 (0.57), residues: 235
  helix:  1.33 (0.38), residues: 206
  sheet:  None (None), residues: 0
  loop : -3.74 (0.80), residues: 29

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.005   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 339 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 1936)
  covalent geometry    : angle       0.54263 ( 2645)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       0.33835 (    2)
  hydrogen bonds       : bond        0.03782 (  132)
  hydrogen bonds       : angle       3.71743 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7931 (tmm) cc_final: 0.7609 (tpp)
REVERT: A  237 ILE cc_start: 0.7853 (tt) cc_final: 0.7540 (tt)
REVERT: A  343 ASN cc_start: 0.7843 (t0) cc_final: 0.7589 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 37
  average time/residue: 0.0434
  time to fit residues: 1.9983
Evaluate side-chains
  37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.127647 restraints weight = 2396.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.50
r_work: 0.3363 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1937  Z= 0.147
  Angle     :  0.557   6.812   2647  Z= 0.290
  Chirality :  0.041   0.178    331
  Planarity :  0.005   0.050    307
  Dihedral  : 11.490 127.957    275
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.10 %
    Favored  : 76.88 %
  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:  1.04 (0.57), residues: 235
  helix:  1.31 (0.38), residues: 206
  sheet:  None (None), residues: 0
  loop : -3.81 (0.78), residues: 29

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.005   0.001   TYR A 380 
 PHE   0.008   0.001   PHE A 339 
 TRP   0.009   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 1936)
  covalent geometry    : angle       0.55750 ( 2645)
  SS BOND              : bond        0.00344 (    1)
  SS BOND              : angle       0.32259 (    2)
  hydrogen bonds       : bond        0.03946 (  132)
  hydrogen bonds       : angle       3.74880 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7842 (tmm) cc_final: 0.7518 (tpp)
REVERT: A  237 ILE cc_start: 0.7727 (tt) cc_final: 0.7414 (tt)
  outliers start: 6
  outliers final: 6
  residues processed: 35
  average time/residue: 0.0463
  time to fit residues: 2.0053
Evaluate side-chains
  36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 11 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.144639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.129071 restraints weight = 2395.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.43
r_work: 0.3390 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   1937  Z= 0.134
  Angle     :  0.547   7.752   2647  Z= 0.285
  Chirality :  0.041   0.182    331
  Planarity :  0.005   0.051    307
  Dihedral  : 11.348 127.460    275
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.60 %
    Favored  : 77.39 %
  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:  1.06 (0.57), residues: 235
  helix:  1.44 (0.39), residues: 201
  sheet:  None (None), residues: 0
  loop : -3.81 (0.67), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.004   0.001   TYR A 153 
 PHE   0.008   0.001   PHE A 243 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 1936)
  covalent geometry    : angle       0.54732 ( 2645)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       0.33886 (    2)
  hydrogen bonds       : bond        0.03734 (  132)
  hydrogen bonds       : angle       3.68474 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7939 (tmm) cc_final: 0.7618 (tpp)
REVERT: A  237 ILE cc_start: 0.7809 (tt) cc_final: 0.7500 (tt)
REVERT: A  343 ASN cc_start: 0.7745 (t0) cc_final: 0.7540 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0459
  time to fit residues: 2.0448
Evaluate side-chains
  37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 6 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.146668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.131799 restraints weight = 2396.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.36
r_work: 0.3414 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1937  Z= 0.125
  Angle     :  0.545   8.927   2647  Z= 0.281
  Chirality :  0.041   0.182    331
  Planarity :  0.005   0.051    307
  Dihedral  : 11.248 127.378    275
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.60 %
    Favored  : 77.39 %
  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 (0.57), residues: 235
  helix:  1.50 (0.39), residues: 201
  sheet:  None (None), residues: 0
  loop : -3.74 (0.69), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.004   0.001   TYR A 153 
 PHE   0.012   0.001   PHE A 125 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 1936)
  covalent geometry    : angle       0.54559 ( 2645)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.31971 (    2)
  hydrogen bonds       : bond        0.03594 (  132)
  hydrogen bonds       : angle       3.62868 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A  237 ILE cc_start: 0.7823 (tt) cc_final: 0.7564 (tt)
REVERT: A  343 ASN cc_start: 0.7728 (t0) cc_final: 0.7495 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 33
  average time/residue: 0.0465
  time to fit residues: 1.8908
Evaluate side-chains
  33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.147677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.132867 restraints weight = 2479.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.44
r_work: 0.3351 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   1937  Z= 0.182
  Angle     :  0.615   9.309   2647  Z= 0.318
  Chirality :  0.043   0.199    331
  Planarity :  0.006   0.050    307
  Dihedral  : 11.735 126.063    275
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.10 %
    Favored  : 76.88 %
  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:  0.76 (0.56), residues: 235
  helix:  1.14 (0.37), residues: 205
  sheet:  None (None), residues: 0
  loop : -3.83 (0.78), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.006   0.001   TYR A 139 
 PHE   0.011   0.001   PHE A 125 
 TRP   0.009   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 1936)
  covalent geometry    : angle       0.61520 ( 2645)
  SS BOND              : bond        0.00504 (    1)
  SS BOND              : angle       0.39787 (    2)
  hydrogen bonds       : bond        0.04362 (  132)
  hydrogen bonds       : angle       3.87455 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A  132 MET cc_start: 0.7962 (tmm) cc_final: 0.7667 (tpp)
REVERT: A  343 ASN cc_start: 0.7968 (t0) cc_final: 0.7696 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0490
  time to fit residues: 1.7596
Evaluate side-chains
  31 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 21 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.146208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130856 restraints weight = 2411.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.44
r_work: 0.3401 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1937  Z= 0.122
  Angle     :  0.564  10.296   2647  Z= 0.289
  Chirality :  0.040   0.180    331
  Planarity :  0.005   0.050    307
  Dihedral  : 11.233 127.373    275
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.11 %
    Favored  : 75.88 %
  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:  1.29 (0.58), residues: 235
  helix:  1.46 (0.38), residues: 206
  sheet:  None (None), residues: 0
  loop : -3.57 (0.86), residues: 29

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 173 
 TYR   0.005   0.001   TYR A 153 
 PHE   0.010   0.001   PHE A 125 
 TRP   0.007   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 1936)
  covalent geometry    : angle       0.56424 ( 2645)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.35145 (    2)
  hydrogen bonds       : bond        0.03483 (  132)
  hydrogen bonds       : angle       3.65660 (  396)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A  237 ILE cc_start: 0.7768 (tt) cc_final: 0.7517 (tt)
REVERT: A  343 ASN cc_start: 0.7644 (t0) cc_final: 0.7410 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.0454
  time to fit residues: 1.9691
Evaluate side-chains
  33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  334 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 9 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0060
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.153670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138743 restraints weight = 2430.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.44
r_work: 0.3408 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1937  Z= 0.127
  Angle     :  0.564   9.841   2647  Z= 0.289
  Chirality :  0.041   0.191    331
  Planarity :  0.005   0.050    307
  Dihedral  : 11.255 127.480    275
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.11 %
    Favored  : 75.88 %
  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:  1.40 (0.58), residues: 235
  helix:  1.53 (0.38), residues: 206
  sheet:  None (None), residues: 0
  loop : -3.49 (0.93), residues: 29

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 173 
 TYR   0.004   0.001   TYR A 370 
 PHE   0.010   0.001   PHE A 125 
 TRP   0.008   0.001   TRP A 367 
 HIS   0.001   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 1936)
  covalent geometry    : angle       0.56383 ( 2645)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.26069 (    2)
  hydrogen bonds       : bond        0.03604 (  132)
  hydrogen bonds       : angle       3.63516 (  396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 705.16 seconds
wall clock time: 13 minutes 12.97 seconds (792.97 seconds total)