Starting phenix.real_space_refine
on Fri Aug 22 14:06:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ck0_16688/08_2025/8ck0_16688.cif"
  }
  resolution = 3.8
  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=   0.003
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      25      5.16       5
     C    2351      2.51       5
     N     659      2.21       5
     O     727      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3762
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3762
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 26, 'TRANS': 451}
          Chain breaks: 2
  Time building chain proxies: 1.17, per 1000 atoms: 0.31
  Number of scatterers: 3762
  At special positions: 0
  Unit cell: (89.1, 94.5, 152.55, 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      25     16.00
     O     727      8.00
     N     659      7.00
     C    2351      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: 0.33
  Conformation dependent library (CDL) restraints added in 166.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  898

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      55.9% alpha, 10.3% 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 5 through 22
    Processing helix  chain 'A' and resid 24 through 35
    Processing helix  chain 'A' and resid 60 through 78
    Processing helix  chain 'A' and resid 91 through 97
      removed outlier: 3.523A  pdb=" N   SER A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 118
    Processing helix  chain 'A' and resid 119 through 135
      removed outlier: 3.553A  pdb=" N   GLN A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 187
    Processing helix  chain 'A' and resid 188 through 192
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 274 through 302
      removed outlier: 4.725A  pdb=" N   GLY A 281 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 4.546A  pdb=" N   LEU A 318 " --> pdb=" O   PRO A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 364
      removed outlier: 4.601A  pdb=" N   ILE A 349 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 4.145A  pdb=" N   THR A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 422
      removed outlier: 3.557A  pdb=" N   GLY A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 467
      removed outlier: 3.569A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 471 through 477
    Processing helix  chain 'A' and resid 479 through 492
      removed outlier: 4.579A  pdb=" N   ASP A 485 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 500 through 523
      removed outlier: 3.819A  pdb=" N   ALA A 518 " --> pdb=" O   GLN A 514 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET A 521 " --> pdb=" O   GLN A 517 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154
      removed outlier: 3.984A  pdb=" N   MET A 154 " --> pdb=" O   CYS A 138 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   CYS A 138 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163
      removed outlier: 9.794A  pdb=" N   ASP A 170 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 306

    214 hydrogen bonds defined for protein.
    600 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: 0.50

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1242
        1.34 -     1.46: 508
        1.46 -     1.57: 2040
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 3836
  Sorted by residual:
  bond pdb=" CA  PRO A 426 "
       pdb=" C   PRO A 426 "
    ideal  model  delta    sigma   weight residual
    1.514  1.534 -0.019 5.50e-03 3.31e+04 1.25e+01
  bond pdb=" C   PRO A 426 "
       pdb=" O   PRO A 426 "
    ideal  model  delta    sigma   weight residual
    1.246  1.218  0.027 8.50e-03 1.38e+04 1.04e+01
  bond pdb=" N   ARG A 150 "
       pdb=" CA  ARG A 150 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.19e-02 7.06e+03 8.35e+00
  bond pdb=" N   ILE A 418 "
       pdb=" CA  ILE A 418 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.18e-02 7.18e+03 7.50e+00
  bond pdb=" N   SER A  40 "
       pdb=" CA  SER A  40 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.29e+00
  ... (remaining 3831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 4972
        1.89 -     3.78: 185
        3.78 -     5.67: 29
        5.67 -     7.56: 4
        7.56 -     9.45: 1
  Bond angle restraints: 5191
  Sorted by residual:
  angle pdb=" CA  PRO A 426 "
        pdb=" C   PRO A 426 "
        pdb=" O   PRO A 426 "
      ideal   model   delta    sigma   weight residual
     120.90  117.93    2.97 7.20e-01 1.93e+00 1.70e+01
  angle pdb=" CA  LYS A 477 "
        pdb=" C   LYS A 477 "
        pdb=" O   LYS A 477 "
      ideal   model   delta    sigma   weight residual
     122.37  118.24    4.13 1.15e+00 7.56e-01 1.29e+01
  angle pdb=" CA  GLU A 143 "
        pdb=" C   GLU A 143 "
        pdb=" O   GLU A 143 "
      ideal   model   delta    sigma   weight residual
     121.99  118.00    3.99 1.14e+00 7.69e-01 1.23e+01
  angle pdb=" CA  ILE A 480 "
        pdb=" C   ILE A 480 "
        pdb=" O   ILE A 480 "
      ideal   model   delta    sigma   weight residual
     121.27  117.78    3.49 1.04e+00 9.25e-01 1.13e+01
  angle pdb=" CA  PRO A 426 "
        pdb=" C   PRO A 426 "
        pdb=" N   PRO A 427 "
      ideal   model   delta    sigma   weight residual
     117.73  120.72   -2.99 9.00e-01 1.23e+00 1.10e+01
  ... (remaining 5186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2036
       17.95 -    35.89: 248
       35.89 -    53.84: 55
       53.84 -    71.78: 10
       71.78 -    89.73: 7
  Dihedral angle restraints: 2356
    sinusoidal: 965
      harmonic: 1391
  Sorted by residual:
  dihedral pdb=" CA  ALA A  81 "
           pdb=" C   ALA A  81 "
           pdb=" N   ARG A  82 "
           pdb=" CA  ARG A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.98  -29.02     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  PRO A  80 "
           pdb=" C   PRO A  80 "
           pdb=" N   ALA A  81 "
           pdb=" CA  ALA A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  VAL A 444 "
           pdb=" C   VAL A 444 "
           pdb=" N   MET A 445 "
           pdb=" CA  MET A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.52   20.48     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 2353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 345
       0.036 -    0.071: 131
       0.071 -    0.107: 55
       0.107 -    0.142: 23
       0.142 -    0.178: 11
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" CA  LEU A 425 "
            pdb=" N   LEU A 425 "
            pdb=" C   LEU A 425 "
            pdb=" CB  LEU A 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CA  ILE A 418 "
            pdb=" N   ILE A 418 "
            pdb=" C   ILE A 418 "
            pdb=" CB  ILE A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  MET A 420 "
            pdb=" N   MET A 420 "
            pdb=" C   MET A 420 "
            pdb=" CB  MET A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 562 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  79 "   -0.095 5.00e-02 4.00e+02   1.43e-01 3.25e+01
        pdb=" N   PRO A  80 "    0.247 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 416 "   -0.025 2.00e-02 2.50e+03   2.55e-02 1.13e+01
        pdb=" CG  PHE A 416 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 416 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 416 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 416 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 416 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 416 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  84 "    0.014 2.00e-02 2.50e+03   1.55e-02 5.99e+00
        pdb=" CG  TRP A  84 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  84 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  84 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  84 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  84 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  84 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  84 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  84 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  84 "    0.001 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 888
        2.79 -     3.32: 3797
        3.32 -     3.84: 6117
        3.84 -     4.37: 6845
        4.37 -     4.90: 11622
  Nonbonded interactions: 29269
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  76 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NH1 ARG A 402 "
            pdb=" OE1 GLU A 406 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   ASP A  46 "
            pdb=" OD1 ASP A  46 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH1 ARG A   7 "
            pdb=" O   GLU A 244 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD1 ASP A 144 "
            pdb=" N   LYS A 145 "
     model   vdw
     2.323 3.120
  ... (remaining 29264 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.570
  Set stop_for_unknowns flag:              0.010
  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:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.760
  Find NCS groups from input model:        0.020
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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      :  0.005   0.066   3836  Z= 0.328
  Angle     :  0.804   9.449   5191  Z= 0.498
  Chirality :  0.052   0.178    565
  Planarity :  0.007   0.143    684
  Dihedral  : 16.634  89.728   1458
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.71 %
    Favored  : 77.29 %
  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:  0.79 (0.39), residues: 472
  helix:  1.61 (0.34), residues: 224
  sheet: -0.28 (0.61), residues: 62
  loop : -0.47 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  67 
 TYR   0.023   0.002   TYR A 325 
 PHE   0.058   0.003   PHE A 416 
 TRP   0.042   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 3836)
  covalent geometry    : angle       0.80449 ( 5191)
  hydrogen bonds       : bond        0.21684 (  214)
  hydrogen bonds       : angle       6.40275 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.9522 (m) cc_final: 0.9203 (t)
REVERT: A  298 GLU cc_start: 0.8180 (tt0) cc_final: 0.7548 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0801
  time to fit residues: 12.4708
Evaluate side-chains
  120 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 324 ASN
A 345 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.097459 restraints weight = 9092.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.100111 restraints weight = 4401.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101936 restraints weight = 2728.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.103135 restraints weight = 1954.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.103849 restraints weight = 1553.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3836  Z= 0.233
  Angle     :  0.651   5.829   5191  Z= 0.342
  Chirality :  0.044   0.173    565
  Planarity :  0.006   0.071    684
  Dihedral  :  4.848  29.072    520
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 18.60 %
    Favored  : 76.09 %
  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:  1.14 (0.39), residues: 472
  helix:  1.62 (0.33), residues: 231
  sheet:  0.18 (0.65), residues: 64
  loop : -0.07 (0.50), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  29 
 TYR   0.014   0.002   TYR A 237 
 PHE   0.009   0.002   PHE A 416 
 TRP   0.025   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 3836)
  covalent geometry    : angle       0.65107 ( 5191)
  hydrogen bonds       : bond        0.04859 (  214)
  hydrogen bonds       : angle       4.85479 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8462 (mt0) cc_final: 0.8120 (mt0)
REVERT: A   27 SER cc_start: 0.9381 (m) cc_final: 0.9101 (t)
REVERT: A   59 ASP cc_start: 0.7732 (t0) cc_final: 0.7474 (t0)
REVERT: A  177 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8122 (ttm-80)
REVERT: A  183 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9364 (mm)
REVERT: A  352 ASP cc_start: 0.8637 (t0) cc_final: 0.8378 (t0)
REVERT: A  414 ARG cc_start: 0.9602 (tpt170) cc_final: 0.9141 (tpt-90)
REVERT: A  521 MET cc_start: 0.5992 (mtt) cc_final: 0.5740 (mtp)
  outliers start: 22
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0586
  time to fit residues: 9.6190
Evaluate side-chains
  127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  445 MET
Chi-restraints excluded: chain A residue  480 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   overall best weight:    3.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 345 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.099064 restraints weight = 8906.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.101774 restraints weight = 4296.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.103570 restraints weight = 2656.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104780 restraints weight = 1909.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.105545 restraints weight = 1519.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3836  Z= 0.144
  Angle     :  0.574   6.887   5191  Z= 0.296
  Chirality :  0.043   0.175    565
  Planarity :  0.004   0.032    684
  Dihedral  :  4.791  24.513    520
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.05 %
    Favored  : 74.88 %
  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:  1.35 (0.40), residues: 472
  helix:  1.72 (0.33), residues: 240
  sheet:  0.43 (0.67), residues: 64
  loop : -0.02 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.013   0.001   TYR A 237 
 PHE   0.009   0.002   PHE A 253 
 TRP   0.026   0.002   TRP A  84 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3836)
  covalent geometry    : angle       0.57420 ( 5191)
  hydrogen bonds       : bond        0.04033 (  214)
  hydrogen bonds       : angle       4.49431 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8389 (mt0) cc_final: 0.8005 (mt0)
REVERT: A   27 SER cc_start: 0.9481 (m) cc_final: 0.9049 (t)
REVERT: A   31 ILE cc_start: 0.9680 (OUTLIER) cc_final: 0.9447 (mt)
REVERT: A   59 ASP cc_start: 0.7846 (t0) cc_final: 0.7544 (t0)
REVERT: A   84 TRP cc_start: 0.8895 (p-90) cc_final: 0.8519 (p-90)
REVERT: A   95 MET cc_start: 0.6967 (mmm) cc_final: 0.6554 (mmm)
REVERT: A  183 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9369 (mm)
REVERT: A  189 LEU cc_start: 0.8965 (tp) cc_final: 0.8754 (tp)
REVERT: A  352 ASP cc_start: 0.8559 (t0) cc_final: 0.8274 (t0)
REVERT: A  414 ARG cc_start: 0.9629 (tpt170) cc_final: 0.9165 (tpt-90)
REVERT: A  521 MET cc_start: 0.5938 (mtt) cc_final: 0.5725 (mtp)
  outliers start: 21
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0547
  time to fit residues: 9.2859
Evaluate side-chains
  127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0870
   chunk 45 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    3.0166

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.119441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099386 restraints weight = 8922.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.102124 restraints weight = 4301.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103953 restraints weight = 2646.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105166 restraints weight = 1893.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.105904 restraints weight = 1503.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3836  Z= 0.143
  Angle     :  0.572   6.145   5191  Z= 0.297
  Chirality :  0.042   0.172    565
  Planarity :  0.004   0.037    684
  Dihedral  :  4.766  24.957    520
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 21.26 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.39), residues: 472
  helix:  1.83 (0.33), residues: 240
  sheet:  0.52 (0.66), residues: 64
  loop :  0.00 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.013   0.001   TYR A 441 
 PHE   0.007   0.001   PHE A  42 
 TRP   0.016   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3836)
  covalent geometry    : angle       0.57236 ( 5191)
  hydrogen bonds       : bond        0.03665 (  214)
  hydrogen bonds       : angle       4.39295 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8440 (mt0) cc_final: 0.8086 (mt0)
REVERT: A   27 SER cc_start: 0.9494 (m) cc_final: 0.9105 (t)
REVERT: A   59 ASP cc_start: 0.7775 (t0) cc_final: 0.7462 (t0)
REVERT: A   95 MET cc_start: 0.6824 (mmm) cc_final: 0.6521 (mmm)
REVERT: A  177 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8076 (ttm-80)
REVERT: A  183 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9347 (mm)
REVERT: A  352 ASP cc_start: 0.8524 (t0) cc_final: 0.8231 (t0)
REVERT: A  414 ARG cc_start: 0.9639 (tpt170) cc_final: 0.9035 (tpp-160)
REVERT: A  521 MET cc_start: 0.5927 (mtt) cc_final: 0.5682 (mtp)
  outliers start: 20
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0564
  time to fit residues: 9.3205
Evaluate side-chains
  126 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0670
   overall best weight:    4.8126

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

Flipped N/Q/H residues before XYZ refinement:
A 345 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.118358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098420 restraints weight = 8983.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.101122 restraints weight = 4357.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.102927 restraints weight = 2699.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104137 restraints weight = 1944.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104916 restraints weight = 1551.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3836  Z= 0.187
  Angle     :  0.609   5.504   5191  Z= 0.311
  Chirality :  0.043   0.168    565
  Planarity :  0.005   0.035    684
  Dihedral  :  4.826  25.041    520
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 22.22 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.39), residues: 472
  helix:  2.01 (0.33), residues: 239
  sheet:  0.30 (0.64), residues: 64
  loop : -0.20 (0.50), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.015   0.001   TYR A 441 
 PHE   0.008   0.001   PHE A  42 
 TRP   0.018   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 3836)
  covalent geometry    : angle       0.60900 ( 5191)
  hydrogen bonds       : bond        0.03725 (  214)
  hydrogen bonds       : angle       4.39177 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8447 (mt0) cc_final: 0.8087 (mt0)
REVERT: A   27 SER cc_start: 0.9373 (m) cc_final: 0.8994 (t)
REVERT: A   31 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9474 (mt)
REVERT: A   59 ASP cc_start: 0.7797 (t0) cc_final: 0.7479 (t0)
REVERT: A   95 MET cc_start: 0.7065 (mmm) cc_final: 0.6669 (mmm)
REVERT: A  183 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9327 (mm)
REVERT: A  189 LEU cc_start: 0.8960 (tp) cc_final: 0.8757 (tp)
REVERT: A  313 SER cc_start: 0.9000 (p) cc_final: 0.8724 (t)
REVERT: A  352 ASP cc_start: 0.8521 (t0) cc_final: 0.8236 (t0)
REVERT: A  414 ARG cc_start: 0.9620 (tpt170) cc_final: 0.9318 (tpt90)
REVERT: A  521 MET cc_start: 0.6056 (mtt) cc_final: 0.5776 (mtp)
  outliers start: 22
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0585
  time to fit residues: 9.5464
Evaluate side-chains
  127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.118612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098784 restraints weight = 9067.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101476 restraints weight = 4356.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103275 restraints weight = 2692.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104380 restraints weight = 1932.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.105160 restraints weight = 1556.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3836  Z= 0.203
  Angle     :  0.612   6.066   5191  Z= 0.315
  Chirality :  0.043   0.168    565
  Planarity :  0.005   0.035    684
  Dihedral  :  4.828  24.259    520
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 21.26 %
    Favored  : 72.95 %
  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:  1.54 (0.39), residues: 472
  helix:  2.16 (0.33), residues: 239
  sheet:  0.27 (0.64), residues: 64
  loop : -0.29 (0.49), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.013   0.001   TYR A 441 
 PHE   0.007   0.001   PHE A  42 
 TRP   0.017   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 3836)
  covalent geometry    : angle       0.61156 ( 5191)
  hydrogen bonds       : bond        0.03675 (  214)
  hydrogen bonds       : angle       4.39750 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8415 (mt0) cc_final: 0.8067 (mt0)
REVERT: A   27 SER cc_start: 0.9375 (m) cc_final: 0.8986 (t)
REVERT: A   31 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9479 (mt)
REVERT: A   59 ASP cc_start: 0.7814 (t0) cc_final: 0.7506 (t0)
REVERT: A   95 MET cc_start: 0.7080 (mmm) cc_final: 0.6643 (mmm)
REVERT: A  183 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9297 (mm)
REVERT: A  189 LEU cc_start: 0.8944 (tp) cc_final: 0.8731 (tp)
REVERT: A  263 TRP cc_start: 0.8944 (t-100) cc_final: 0.8246 (t-100)
REVERT: A  313 SER cc_start: 0.9034 (p) cc_final: 0.8746 (t)
REVERT: A  352 ASP cc_start: 0.8521 (t0) cc_final: 0.8242 (t0)
REVERT: A  414 ARG cc_start: 0.9629 (tpt170) cc_final: 0.9318 (tpt90)
REVERT: A  521 MET cc_start: 0.6090 (mtt) cc_final: 0.5817 (mtp)
  outliers start: 24
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0553
  time to fit residues: 8.8182
Evaluate side-chains
  126 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.119012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099128 restraints weight = 9067.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101855 restraints weight = 4390.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103672 restraints weight = 2719.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.104855 restraints weight = 1956.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.105617 restraints weight = 1562.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3836  Z= 0.178
  Angle     :  0.608   7.116   5191  Z= 0.312
  Chirality :  0.043   0.167    565
  Planarity :  0.004   0.035    684
  Dihedral  :  4.823  23.353    520
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 20.77 %
    Favored  : 73.43 %
  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:  1.73 (0.39), residues: 472
  helix:  2.32 (0.33), residues: 237
  sheet:  0.37 (0.63), residues: 64
  loop : -0.18 (0.49), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.013   0.001   TYR A 441 
 PHE   0.005   0.001   PHE A 253 
 TRP   0.021   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3836)
  covalent geometry    : angle       0.60810 ( 5191)
  hydrogen bonds       : bond        0.03563 (  214)
  hydrogen bonds       : angle       4.35185 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8406 (mt0) cc_final: 0.8050 (mt0)
REVERT: A   27 SER cc_start: 0.9370 (m) cc_final: 0.8977 (t)
REVERT: A   31 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9479 (mt)
REVERT: A   59 ASP cc_start: 0.7838 (t0) cc_final: 0.7518 (t0)
REVERT: A   95 MET cc_start: 0.6855 (mmm) cc_final: 0.6452 (mmm)
REVERT: A  183 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9304 (mm)
REVERT: A  189 LEU cc_start: 0.8920 (tp) cc_final: 0.8709 (tp)
REVERT: A  204 ASN cc_start: 0.8285 (t0) cc_final: 0.7650 (p0)
REVERT: A  263 TRP cc_start: 0.8970 (t-100) cc_final: 0.8265 (t-100)
REVERT: A  313 SER cc_start: 0.9049 (p) cc_final: 0.8746 (t)
REVERT: A  352 ASP cc_start: 0.8500 (t0) cc_final: 0.8218 (t0)
REVERT: A  401 GLU cc_start: 0.7294 (pm20) cc_final: 0.6733 (pt0)
REVERT: A  414 ARG cc_start: 0.9609 (tpt170) cc_final: 0.9387 (tpt90)
REVERT: A  521 MET cc_start: 0.6082 (mtt) cc_final: 0.5815 (mtp)
  outliers start: 24
  outliers final: 20
  residues processed: 124
  average time/residue: 0.0545
  time to fit residues: 8.6093
Evaluate side-chains
  131 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.119318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.099486 restraints weight = 9261.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.102195 restraints weight = 4466.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.104002 restraints weight = 2764.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105206 restraints weight = 1982.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105918 restraints weight = 1580.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3836  Z= 0.236
  Angle     :  0.672   9.749   5191  Z= 0.342
  Chirality :  0.044   0.169    565
  Planarity :  0.005   0.036    684
  Dihedral  :  4.925  23.589    520
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 20.77 %
    Favored  : 73.19 %
  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:  1.65 (0.39), residues: 472
  helix:  2.31 (0.34), residues: 239
  sheet:  0.41 (0.65), residues: 64
  loop : -0.40 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.014   0.002   TYR A 441 
 PHE   0.010   0.002   PHE A  42 
 TRP   0.020   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 3836)
  covalent geometry    : angle       0.67152 ( 5191)
  hydrogen bonds       : bond        0.03789 (  214)
  hydrogen bonds       : angle       4.44285 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8388 (mt0) cc_final: 0.8035 (mt0)
REVERT: A   27 SER cc_start: 0.9360 (m) cc_final: 0.8945 (t)
REVERT: A   31 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9505 (mt)
REVERT: A   59 ASP cc_start: 0.7847 (t0) cc_final: 0.7545 (t0)
REVERT: A   95 MET cc_start: 0.6880 (mmm) cc_final: 0.6482 (mmm)
REVERT: A  103 TRP cc_start: 0.9064 (t60) cc_final: 0.8703 (t60)
REVERT: A  183 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9281 (mm)
REVERT: A  204 ASN cc_start: 0.8317 (t0) cc_final: 0.7692 (p0)
REVERT: A  263 TRP cc_start: 0.8993 (t-100) cc_final: 0.8292 (t-100)
REVERT: A  352 ASP cc_start: 0.8533 (t0) cc_final: 0.8264 (t0)
REVERT: A  401 GLU cc_start: 0.7375 (pm20) cc_final: 0.6898 (pt0)
REVERT: A  414 ARG cc_start: 0.9660 (tpt170) cc_final: 0.9271 (tpp-160)
REVERT: A  521 MET cc_start: 0.6148 (mtt) cc_final: 0.5905 (mtp)
REVERT: A  523 MET cc_start: 0.4615 (ttt) cc_final: 0.4354 (ttp)
  outliers start: 25
  outliers final: 23
  residues processed: 121
  average time/residue: 0.0603
  time to fit residues: 9.3419
Evaluate side-chains
  130 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.8584

-------------------------------------------------------------------------------
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 = 0.3622 r_free = 0.3622 target = 0.122507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.103006 restraints weight = 8964.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.105812 restraints weight = 4309.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.107644 restraints weight = 2645.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.108780 restraints weight = 1888.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.109600 restraints weight = 1509.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3836  Z= 0.115
  Angle     :  0.617   9.385   5191  Z= 0.307
  Chirality :  0.042   0.170    565
  Planarity :  0.004   0.034    684
  Dihedral  :  4.728  21.653    520
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 24.15 %
    Favored  : 71.74 %
  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 (0.40), residues: 472
  helix:  2.50 (0.33), residues: 237
  sheet:  0.72 (0.68), residues: 62
  loop : -0.11 (0.49), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.011   0.001   TYR A 237 
 PHE   0.009   0.001   PHE A  42 
 TRP   0.024   0.001   TRP A  84 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3836)
  covalent geometry    : angle       0.61721 ( 5191)
  hydrogen bonds       : bond        0.03260 (  214)
  hydrogen bonds       : angle       4.24791 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8398 (mt0) cc_final: 0.8055 (mt0)
REVERT: A   27 SER cc_start: 0.9479 (m) cc_final: 0.9046 (t)
REVERT: A   59 ASP cc_start: 0.7874 (t0) cc_final: 0.7632 (t0)
REVERT: A   93 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5838 (mm-30)
REVERT: A   95 MET cc_start: 0.6895 (mmm) cc_final: 0.6529 (mmm)
REVERT: A  103 TRP cc_start: 0.8913 (t60) cc_final: 0.8411 (t60)
REVERT: A  183 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9190 (mm)
REVERT: A  189 LEU cc_start: 0.8997 (tp) cc_final: 0.8764 (tp)
REVERT: A  201 ASP cc_start: 0.9134 (m-30) cc_final: 0.8290 (p0)
REVERT: A  204 ASN cc_start: 0.8252 (t0) cc_final: 0.7672 (p0)
REVERT: A  313 SER cc_start: 0.9007 (p) cc_final: 0.8678 (t)
REVERT: A  352 ASP cc_start: 0.8436 (t0) cc_final: 0.8151 (t0)
REVERT: A  401 GLU cc_start: 0.7230 (pm20) cc_final: 0.6525 (pt0)
REVERT: A  414 ARG cc_start: 0.9559 (tpt170) cc_final: 0.9093 (tpp-160)
REVERT: A  421 ARG cc_start: 0.8530 (mmt90) cc_final: 0.8311 (mpt-90)
REVERT: A  521 MET cc_start: 0.6120 (mtt) cc_final: 0.5871 (mtp)
  outliers start: 17
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0526
  time to fit residues: 8.3070
Evaluate side-chains
  128 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0070
   chunk 44 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.4602

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.122494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103018 restraints weight = 9182.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.105812 restraints weight = 4360.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.107628 restraints weight = 2676.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.108811 restraints weight = 1910.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.109610 restraints weight = 1520.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3836  Z= 0.130
  Angle     :  0.637  12.243   5191  Z= 0.314
  Chirality :  0.042   0.169    565
  Planarity :  0.004   0.036    684
  Dihedral  :  4.664  20.899    520
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.67 %
    Favored  : 72.71 %
  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:  1.93 (0.40), residues: 472
  helix:  2.46 (0.33), residues: 237
  sheet:  0.58 (0.68), residues: 64
  loop : -0.10 (0.49), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 177 
 TYR   0.010   0.001   TYR A 237 
 PHE   0.016   0.002   PHE A 416 
 TRP   0.022   0.001   TRP A  84 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3836)
  covalent geometry    : angle       0.63679 ( 5191)
  hydrogen bonds       : bond        0.03375 (  214)
  hydrogen bonds       : angle       4.23941 (  600)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8447 (mt0) cc_final: 0.8149 (mt0)
REVERT: A   27 SER cc_start: 0.9477 (m) cc_final: 0.9050 (t)
REVERT: A   59 ASP cc_start: 0.7767 (t0) cc_final: 0.7496 (t0)
REVERT: A   93 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5854 (mm-30)
REVERT: A   95 MET cc_start: 0.6845 (mmm) cc_final: 0.6468 (mmm)
REVERT: A  183 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9181 (mm)
REVERT: A  189 LEU cc_start: 0.8861 (tp) cc_final: 0.8621 (tp)
REVERT: A  201 ASP cc_start: 0.9134 (m-30) cc_final: 0.8284 (p0)
REVERT: A  204 ASN cc_start: 0.8228 (t0) cc_final: 0.7657 (p0)
REVERT: A  352 ASP cc_start: 0.8423 (t0) cc_final: 0.8134 (t0)
REVERT: A  401 GLU cc_start: 0.7189 (pm20) cc_final: 0.6559 (pt0)
REVERT: A  414 ARG cc_start: 0.9534 (tpt170) cc_final: 0.8916 (tpp-160)
REVERT: A  521 MET cc_start: 0.6148 (mtt) cc_final: 0.5893 (mtp)
  outliers start: 15
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0503
  time to fit residues: 7.6343
Evaluate side-chains
  120 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0000
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.123541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.104588 restraints weight = 9049.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107316 restraints weight = 4289.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109083 restraints weight = 2620.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.110231 restraints weight = 1862.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110919 restraints weight = 1480.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3836  Z= 0.113
  Angle     :  0.630   9.755   5191  Z= 0.316
  Chirality :  0.042   0.171    565
  Planarity :  0.004   0.035    684
  Dihedral  :  4.479  17.227    520
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 23.91 %
    Favored  : 72.95 %
  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:  2.05 (0.40), residues: 472
  helix:  2.54 (0.33), residues: 237
  sheet:  0.74 (0.70), residues: 62
  loop : -0.05 (0.50), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.011   0.001   TYR A 237 
 PHE   0.031   0.002   PHE A 416 
 TRP   0.024   0.001   TRP A  84 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3836)
  covalent geometry    : angle       0.63040 ( 5191)
  hydrogen bonds       : bond        0.03071 (  214)
  hydrogen bonds       : angle       4.15660 (  600)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 848.35 seconds
wall clock time: 15 minutes 20.99 seconds (920.99 seconds total)