Starting phenix.real_space_refine
on Tue Mar  3 11:36:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t01_25574/03_2026/7t01_25574.cif"
  }
  resolution = 2.69
  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=   0.015
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      16      5.16       5
     C    2136      2.51       5
     N     555      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3343
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 6, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
  Time building chain proxies: 1.10, per 1000 atoms: 0.33
  Number of scatterers: 3343
  At special positions: 0
  Unit cell: (68.85, 62.37, 101.25, 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      16     16.00
     O     636      8.00
     N     555      7.00
     C    2136      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.04

  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: 0.17
  Conformation dependent library (CDL) restraints added in 89.7 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  790

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      13.1% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 4.007A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.380A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.572A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 66
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'L' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.297A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.732A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.596A  pdb=" N   GLN H  79 " --> pdb=" O   ASP H  74 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR H  70 " --> pdb=" O   THR H  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 59 through 61
      removed outlier: 6.602A  pdb=" N   TRP H  38 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   LEU H  52 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL H  36 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   TYR H  54 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL H  34 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL H 112 " --> pdb=" O   HIS H  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 61
      removed outlier: 6.602A  pdb=" N   TRP H  38 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   LEU H  52 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL H  36 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   TYR H  54 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL H  34 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.714A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.722A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA L  50 " --> pdb=" O   ARG L  53 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    255 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: 0.41

  Time building geometry restraints manager: 0.24 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: 1049
        1.34 -     1.46: 894
        1.46 -     1.59: 1469
        1.59 -     1.71: 0
        1.71 -     1.83: 20
  Bond restraints: 3432
  Sorted by residual:
  bond pdb=" C   THR L  94 "
       pdb=" N   PRO L  95 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.75e+00
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.031 2.34e-02 1.83e+03 1.75e+00
  bond pdb=" C   LYS H  13 "
       pdb=" N   PRO H  14 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.07e+00
  bond pdb=" CB  ILE L  48 "
       pdb=" CG2 ILE L  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" C   ALA A 520 "
       pdb=" N   PRO A 521 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 1.00e+00
  ... (remaining 3427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 4592
        2.62 -     5.24: 69
        5.24 -     7.86: 10
        7.86 -    10.48: 1
       10.48 -    13.09: 1
  Bond angle restraints: 4673
  Sorted by residual:
  angle pdb=" CA  LEU H  29 "
        pdb=" CB  LEU H  29 "
        pdb=" CG  LEU H  29 "
      ideal   model   delta    sigma   weight residual
     116.30  129.39  -13.09 3.50e+00 8.16e-02 1.40e+01
  angle pdb=" CA  TYR L  49 "
        pdb=" CB  TYR L  49 "
        pdb=" CG  TYR L  49 "
      ideal   model   delta    sigma   weight residual
     113.90  120.52   -6.62 1.80e+00 3.09e-01 1.35e+01
  angle pdb=" CA  VAL L  29 "
        pdb=" CB  VAL L  29 "
        pdb=" CG1 VAL L  29 "
      ideal   model   delta    sigma   weight residual
     110.40  116.34   -5.94 1.70e+00 3.46e-01 1.22e+01
  angle pdb=" N   VAL L  29 "
        pdb=" CA  VAL L  29 "
        pdb=" CB  VAL L  29 "
      ideal   model   delta    sigma   weight residual
     112.08  107.07    5.01 1.68e+00 3.54e-01 8.90e+00
  angle pdb=" C   TYR L  49 "
        pdb=" CA  TYR L  49 "
        pdb=" CB  TYR L  49 "
      ideal   model   delta    sigma   weight residual
     110.90  106.38    4.52 1.58e+00 4.01e-01 8.19e+00
  ... (remaining 4668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 1810
       14.74 -    29.48: 171
       29.48 -    44.22: 29
       44.22 -    58.96: 5
       58.96 -    73.70: 4
  Dihedral angle restraints: 2019
    sinusoidal: 781
      harmonic: 1238
  Sorted by residual:
  dihedral pdb=" CA  TYR H  54 "
           pdb=" C   TYR H  54 "
           pdb=" N   TRP H  55 "
           pdb=" CA  TRP H  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  SER L   9 "
           pdb=" C   SER L   9 "
           pdb=" N   SER L  10 "
           pdb=" CA  SER L  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.91   27.09     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  LEU L  78 "
           pdb=" C   LEU L  78 "
           pdb=" N   GLN L  79 "
           pdb=" CA  GLN L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.01   26.99     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 2016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 311
       0.043 -    0.085: 143
       0.085 -    0.128: 51
       0.128 -    0.171: 8
       0.171 -    0.214: 2
  Chirality restraints: 515
  Sorted by residual:
  chirality pdb=" CA  THR L  94 "
            pdb=" N   THR L  94 "
            pdb=" C   THR L  94 "
            pdb=" CB  THR L  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA ASER L   7 "
            pdb=" N   SER L   7 "
            pdb=" C   SER L   7 "
            pdb=" CB ASER L   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CA  PRO H  14 "
            pdb=" N   PRO H  14 "
            pdb=" C   PRO H  14 "
            pdb=" CB  PRO H  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 512 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  49 "   -0.025 2.00e-02 2.50e+03   2.08e-02 8.61e+00
        pdb=" CG  TYR L  49 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  49 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  49 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  49 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  49 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR L  49 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  29 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   VAL L  29 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL L  29 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE L  30 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  60 "   -0.167 9.50e-02 1.11e+02   7.55e-02 4.40e+00
        pdb=" NE  ARG H  60 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  60 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  60 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  60 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1135
        2.85 -     3.36: 3020
        3.36 -     3.87: 5498
        3.87 -     4.39: 6364
        4.39 -     4.90: 10848
  Nonbonded interactions: 26865
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP H  74 "
            pdb=" OG  SER H  76 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ALA L  25 "
            pdb=" OG1 THR L  69 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" ND2 ASN A 394 "
            pdb=" OE2 GLU A 516 "
     model   vdw
     2.419 3.120
  nonbonded pdb=" OG  SER A 438 "
            pdb=" OD2 ASP A 442 "
     model   vdw
     2.485 3.040
  nonbonded pdb=" NH1 ARG H  60 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.508 3.120
  ... (remaining 26860 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.480
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
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      :  0.004   0.039   3435  Z= 0.168
  Angle     :  0.871  13.094   4679  Z= 0.469
  Chirality :  0.054   0.214    515
  Planarity :  0.008   0.075    598
  Dihedral  : 12.300  73.703   1220
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.38), residues: 422
  helix: -3.82 (0.72), residues: 19
  sheet: -0.35 (0.44), residues: 125
  loop : -0.63 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.003   ARG H  60 
 TYR   0.047   0.005   TYR L  49 
 PHE   0.020   0.002   PHE L  83 
 TRP   0.025   0.002   TRP A 436 
 HIS   0.002   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3432)
  covalent geometry    : angle       0.87023 ( 4673)
  SS BOND              : bond        0.00511 (    3)
  SS BOND              : angle       1.36598 (    6)
  hydrogen bonds       : bond        0.20648 (   98)
  hydrogen bonds       : angle       9.60190 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8549 (m) cc_final: 0.8312 (p)
REVERT: A  362 VAL cc_start: 0.8512 (t) cc_final: 0.8165 (p)
REVERT: A  421 TYR cc_start: 0.8398 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  425 LEU cc_start: 0.8830 (mt) cc_final: 0.8604 (mt)
REVERT: A  442 ASP cc_start: 0.8082 (m-30) cc_final: 0.7821 (m-30)
REVERT: A  454 ARG cc_start: 0.9020 (ttm-80) cc_final: 0.8736 (ttm110)
REVERT: A  456 PHE cc_start: 0.7839 (m-80) cc_final: 0.7590 (m-80)
REVERT: H   61 TYR cc_start: 0.8953 (m-80) cc_final: 0.8675 (m-80)
REVERT: L    2 MET cc_start: 0.8511 (tpt) cc_final: 0.8181 (tpt)
REVERT: L   14 SER cc_start: 0.8801 (m) cc_final: 0.8560 (m)
REVERT: L   22 THR cc_start: 0.7998 (p) cc_final: 0.7726 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.3888
  time to fit residues: 68.0740
Evaluate side-chains
  149 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0770
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
L   3 GLN
L  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.089672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.077284 restraints weight = 7314.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.91
r_work: 0.3206 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3435  Z= 0.254
  Angle     :  0.788   9.456   4679  Z= 0.397
  Chirality :  0.051   0.204    515
  Planarity :  0.005   0.035    598
  Dihedral  :  6.683  24.845    465
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.84 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.37), residues: 422
  helix: -2.59 (1.53), residues: 12
  sheet: -0.22 (0.45), residues: 123
  loop : -0.85 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  68 
 TYR   0.012   0.002   TYR L  49 
 PHE   0.021   0.002   PHE L  83 
 TRP   0.020   0.003   TRP A 436 
 HIS   0.003   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 3432)
  covalent geometry    : angle       0.78759 ( 4673)
  SS BOND              : bond        0.00428 (    3)
  SS BOND              : angle       0.79905 (    6)
  hydrogen bonds       : bond        0.03549 (   98)
  hydrogen bonds       : angle       6.28608 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8384 (ttp-170)
REVERT: A  362 VAL cc_start: 0.8750 (t) cc_final: 0.8503 (p)
REVERT: A  425 LEU cc_start: 0.8997 (mt) cc_final: 0.8725 (mt)
REVERT: A  442 ASP cc_start: 0.8544 (m-30) cc_final: 0.8247 (m-30)
REVERT: A  454 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8865 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8007 (m-80) cc_final: 0.7723 (m-80)
REVERT: A  489 TYR cc_start: 0.7911 (m-80) cc_final: 0.7698 (m-10)
REVERT: H   27 PHE cc_start: 0.8898 (p90) cc_final: 0.8687 (p90)
REVERT: H   61 TYR cc_start: 0.9086 (m-80) cc_final: 0.8844 (m-80)
REVERT: L   18 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8390 (ttm170)
REVERT: L   55 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8677 (tm-30)
REVERT: L   61 ARG cc_start: 0.8857 (ptt-90) cc_final: 0.8632 (ptt-90)
  outliers start: 14
  outliers final: 6
  residues processed: 157
  average time/residue: 0.3786
  time to fit residues: 61.6784
Evaluate side-chains
  146 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.087575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.075709 restraints weight = 7432.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.86
r_work: 0.3189 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3435  Z= 0.254
  Angle     :  0.769  11.224   4679  Z= 0.387
  Chirality :  0.051   0.200    515
  Planarity :  0.005   0.046    598
  Dihedral  :  6.346  24.573    465
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 23.86 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.38), residues: 422
  helix: -2.27 (1.68), residues: 12
  sheet: -0.32 (0.47), residues: 114
  loop : -0.89 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  60 
 TYR   0.014   0.002   TYR L  87 
 PHE   0.017   0.002   PHE H  24 
 TRP   0.021   0.002   TRP H  55 
 HIS   0.003   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 3432)
  covalent geometry    : angle       0.76925 ( 4673)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.53014 (    6)
  hydrogen bonds       : bond        0.03378 (   98)
  hydrogen bonds       : angle       5.90170 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8685 (ttm170) cc_final: 0.8430 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8489 (ptm-80)
REVERT: A  425 LEU cc_start: 0.8980 (mt) cc_final: 0.8708 (mt)
REVERT: A  442 ASP cc_start: 0.8674 (m-30) cc_final: 0.8362 (m-30)
REVERT: A  454 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8742 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8083 (m-80) cc_final: 0.7809 (m-80)
REVERT: H  119 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8864 (p)
REVERT: L   55 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8670 (tm-30)
REVERT: L   90 GLN cc_start: 0.8909 (pp30) cc_final: 0.8620 (pp30)
  outliers start: 23
  outliers final: 10
  residues processed: 161
  average time/residue: 0.3968
  time to fit residues: 66.1080
Evaluate side-chains
  156 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   88 ASP
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 28 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.087133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.075293 restraints weight = 7443.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.86
r_work: 0.3185 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3435  Z= 0.243
  Angle     :  0.786  11.932   4679  Z= 0.389
  Chirality :  0.050   0.195    515
  Planarity :  0.005   0.046    598
  Dihedral  :  6.198  22.961    465
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  7.51 %
    Allowed  : 26.27 %
    Favored  : 66.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.39), residues: 422
  helix: -2.16 (1.74), residues: 12
  sheet: -0.32 (0.48), residues: 116
  loop : -0.96 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  61 
 TYR   0.010   0.002   TYR A 421 
 PHE   0.029   0.002   PHE H  27 
 TRP   0.039   0.003   TRP H  55 
 HIS   0.005   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 3432)
  covalent geometry    : angle       0.78631 ( 4673)
  SS BOND              : bond        0.00421 (    3)
  SS BOND              : angle       0.37544 (    6)
  hydrogen bonds       : bond        0.03283 (   98)
  hydrogen bonds       : angle       5.77857 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8689 (ttm170) cc_final: 0.8471 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8481 (ptm-80)
REVERT: A  425 LEU cc_start: 0.8940 (mt) cc_final: 0.8700 (mt)
REVERT: A  442 ASP cc_start: 0.8674 (m-30) cc_final: 0.8401 (m-30)
REVERT: A  454 ARG cc_start: 0.9206 (ttm-80) cc_final: 0.8794 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8084 (m-80) cc_final: 0.7839 (m-80)
REVERT: H   81 VAL cc_start: 0.9303 (m) cc_final: 0.9025 (p)
REVERT: H   84 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8430 (tm)
REVERT: L   18 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8593 (ptm160)
REVERT: L   55 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8732 (tm-30)
REVERT: L   82 ASP cc_start: 0.8140 (m-30) cc_final: 0.7880 (m-30)
REVERT: L   90 GLN cc_start: 0.8956 (pp30) cc_final: 0.8674 (pp30)
  outliers start: 28
  outliers final: 11
  residues processed: 151
  average time/residue: 0.4131
  time to fit residues: 64.5659
Evaluate side-chains
  155 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0000
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 35 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0980
   overall best weight:    0.1584

-------------------------------------------------------------------------------
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 = 0.090529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.078682 restraints weight = 7406.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.91
r_work: 0.3251 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3435  Z= 0.129
  Angle     :  0.751  11.521   4679  Z= 0.367
  Chirality :  0.048   0.172    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.609  23.555    465
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 28.42 %
    Favored  : 64.88 %
  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 are not related in a simple way.
  whole: -1.30 (0.39), residues: 422
  helix: -2.03 (1.84), residues: 12
  sheet: -0.72 (0.46), residues: 127
  loop : -0.87 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  61 
 TYR   0.010   0.001   TYR L  36 
 PHE   0.042   0.002   PHE H  27 
 TRP   0.025   0.002   TRP H  55 
 HIS   0.003   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3432)
  covalent geometry    : angle       0.75172 ( 4673)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.28492 (    6)
  hydrogen bonds       : bond        0.02952 (   98)
  hydrogen bonds       : angle       5.45608 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8402 (t)
REVERT: A  390 LEU cc_start: 0.8839 (mm) cc_final: 0.8638 (mp)
REVERT: A  408 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8508 (ptm-80)
REVERT: A  409 GLN cc_start: 0.8978 (mt0) cc_final: 0.8703 (tt0)
REVERT: A  425 LEU cc_start: 0.8902 (mt) cc_final: 0.8650 (mt)
REVERT: A  442 ASP cc_start: 0.8659 (m-30) cc_final: 0.8349 (m-30)
REVERT: A  454 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8868 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8011 (m-80) cc_final: 0.7758 (m-80)
REVERT: H   20 LEU cc_start: 0.8689 (mp) cc_final: 0.8422 (mp)
REVERT: H   38 TRP cc_start: 0.8630 (m100) cc_final: 0.8391 (m100)
REVERT: H   81 VAL cc_start: 0.9245 (m) cc_final: 0.8966 (p)
REVERT: L   18 ARG cc_start: 0.8806 (ttm170) cc_final: 0.8567 (ptm160)
REVERT: L   55 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8518 (tm-30)
REVERT: L   82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7889 (m-30)
REVERT: L   86 TYR cc_start: 0.8248 (m-80) cc_final: 0.7939 (m-10)
  outliers start: 25
  outliers final: 11
  residues processed: 162
  average time/residue: 0.3971
  time to fit residues: 66.5339
Evaluate side-chains
  161 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.0270
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0570
   chunk 20 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.3756

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.088780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.076916 restraints weight = 7441.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.91
r_work: 0.3220 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3435  Z= 0.183
  Angle     :  0.790  12.256   4679  Z= 0.381
  Chirality :  0.049   0.181    515
  Planarity :  0.005   0.042    598
  Dihedral  :  5.661  23.675    465
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 31.37 %
    Favored  : 63.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.40), residues: 422
  helix: -1.83 (1.94), residues: 12
  sheet: -0.69 (0.47), residues: 127
  loop : -0.89 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  61 
 TYR   0.013   0.001   TYR L  36 
 PHE   0.028   0.002   PHE H  27 
 TRP   0.024   0.002   TRP H  55 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3432)
  covalent geometry    : angle       0.78923 ( 4673)
  SS BOND              : bond        0.00626 (    3)
  SS BOND              : angle       1.08244 (    6)
  hydrogen bonds       : bond        0.03035 (   98)
  hydrogen bonds       : angle       5.36837 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8426 (t)
REVERT: A  390 LEU cc_start: 0.8917 (mm) cc_final: 0.8697 (mp)
REVERT: A  408 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8529 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9003 (mt0) cc_final: 0.8744 (tt0)
REVERT: A  442 ASP cc_start: 0.8651 (m-30) cc_final: 0.8357 (m-30)
REVERT: A  454 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8915 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8028 (m-80) cc_final: 0.7767 (m-80)
REVERT: H   81 VAL cc_start: 0.9246 (m) cc_final: 0.8964 (p)
REVERT: L   18 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8405 (ptm160)
REVERT: L   55 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8618 (tm-30)
REVERT: L   75 ILE cc_start: 0.8732 (mp) cc_final: 0.8426 (tp)
REVERT: L   82 ASP cc_start: 0.8109 (m-30) cc_final: 0.7829 (m-30)
REVERT: L   90 GLN cc_start: 0.8937 (pp30) cc_final: 0.8700 (pp30)
  outliers start: 21
  outliers final: 12
  residues processed: 156
  average time/residue: 0.3870
  time to fit residues: 62.7173
Evaluate side-chains
  155 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.3838

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.088687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076903 restraints weight = 7525.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.93
r_work: 0.3218 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3435  Z= 0.185
  Angle     :  0.802  12.408   4679  Z= 0.386
  Chirality :  0.050   0.186    515
  Planarity :  0.005   0.042    598
  Dihedral  :  5.642  23.966    465
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 33.51 %
    Favored  : 61.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.40), residues: 422
  helix: -2.00 (1.86), residues: 12
  sheet: -0.68 (0.47), residues: 127
  loop : -0.92 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  61 
 TYR   0.013   0.002   TYR L  36 
 PHE   0.025   0.002   PHE L  71 
 TRP   0.030   0.003   TRP H  55 
 HIS   0.001   0.000   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 3432)
  covalent geometry    : angle       0.80139 ( 4673)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       1.13635 (    6)
  hydrogen bonds       : bond        0.03063 (   98)
  hydrogen bonds       : angle       5.34491 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8414 (t)
REVERT: A  408 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9019 (mt0) cc_final: 0.8706 (tt0)
REVERT: A  442 ASP cc_start: 0.8676 (m-30) cc_final: 0.8377 (m-30)
REVERT: A  454 ARG cc_start: 0.9194 (ttm-80) cc_final: 0.8888 (ttm-80)
REVERT: A  467 ASP cc_start: 0.8260 (p0) cc_final: 0.7991 (p0)
REVERT: L   55 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8600 (tm-30)
REVERT: L   90 GLN cc_start: 0.8965 (pp30) cc_final: 0.8756 (pp30)
  outliers start: 19
  outliers final: 12
  residues processed: 151
  average time/residue: 0.3800
  time to fit residues: 59.5059
Evaluate side-chains
  157 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0570
   chunk 35 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 18 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.3498

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.088737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.076831 restraints weight = 7600.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.97
r_work: 0.3222 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   3435  Z= 0.183
  Angle     :  0.839  12.569   4679  Z= 0.402
  Chirality :  0.050   0.183    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.675  23.931    465
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 34.05 %
    Favored  : 60.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.40), residues: 422
  helix: -2.05 (1.84), residues: 12
  sheet: -0.86 (0.47), residues: 127
  loop : -0.91 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  61 
 TYR   0.025   0.002   TYR A 489 
 PHE   0.023   0.002   PHE H  27 
 TRP   0.036   0.003   TRP H  55 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 3432)
  covalent geometry    : angle       0.83877 ( 4673)
  SS BOND              : bond        0.00483 (    3)
  SS BOND              : angle       1.01639 (    6)
  hydrogen bonds       : bond        0.03437 (   98)
  hydrogen bonds       : angle       5.47306 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8426 (t)
REVERT: A  408 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8534 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9022 (mt0) cc_final: 0.8718 (tt0)
REVERT: A  442 ASP cc_start: 0.8673 (m-30) cc_final: 0.8383 (m-30)
REVERT: A  454 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8937 (ttm-80)
REVERT: L   55 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8563 (tm-30)
REVERT: L   82 ASP cc_start: 0.8084 (m-30) cc_final: 0.7787 (m-30)
REVERT: L   90 GLN cc_start: 0.9004 (pp30) cc_final: 0.8795 (pp30)
  outliers start: 19
  outliers final: 11
  residues processed: 149
  average time/residue: 0.3989
  time to fit residues: 61.6049
Evaluate side-chains
  162 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain L residue   97 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0770
   chunk 11 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0770
   overall best weight:    0.3296

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.089136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.077188 restraints weight = 7396.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.95
r_work: 0.3226 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   3435  Z= 0.179
  Angle     :  0.849  12.822   4679  Z= 0.407
  Chirality :  0.051   0.275    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.646  23.754    465
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 36.19 %
    Favored  : 60.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.40), residues: 422
  helix: -2.07 (1.83), residues: 12
  sheet: -0.94 (0.47), residues: 127
  loop : -0.91 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  61 
 TYR   0.020   0.002   TYR A 489 
 PHE   0.022   0.002   PHE H  27 
 TRP   0.041   0.003   TRP H  55 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 3432)
  covalent geometry    : angle       0.84876 ( 4673)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       1.11083 (    6)
  hydrogen bonds       : bond        0.03491 (   98)
  hydrogen bonds       : angle       5.43152 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8416 (t)
REVERT: A  408 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8532 (ptm-80)
REVERT: A  409 GLN cc_start: 0.8991 (mt0) cc_final: 0.8681 (tt0)
REVERT: A  442 ASP cc_start: 0.8656 (m-30) cc_final: 0.8359 (m-30)
REVERT: A  454 ARG cc_start: 0.9187 (ttm-80) cc_final: 0.8900 (ttm-80)
REVERT: A  467 ASP cc_start: 0.8183 (p0) cc_final: 0.7969 (p0)
REVERT: H   81 VAL cc_start: 0.9229 (m) cc_final: 0.8928 (p)
REVERT: L   55 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8600 (tm-30)
REVERT: L   81 GLU cc_start: 0.8667 (pm20) cc_final: 0.8275 (pm20)
REVERT: L   82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7606 (m-30)
REVERT: L   90 GLN cc_start: 0.9035 (pp30) cc_final: 0.8821 (pp30)
  outliers start: 12
  outliers final: 7
  residues processed: 143
  average time/residue: 0.3962
  time to fit residues: 58.6625
Evaluate side-chains
  144 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0040
   chunk 17 optimal weight:    0.0870
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.2370

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.090620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.078550 restraints weight = 7343.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.99
r_work: 0.3248 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3435  Z= 0.159
  Angle     :  0.866  12.728   4679  Z= 0.412
  Chirality :  0.050   0.257    515
  Planarity :  0.005   0.061    598
  Dihedral  :  5.555  24.253    465
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 37.00 %
    Favored  : 60.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.41), residues: 422
  helix: -2.18 (1.77), residues: 12
  sheet: -0.95 (0.46), residues: 127
  loop : -0.82 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  61 
 TYR   0.023   0.002   TYR A 489 
 PHE   0.025   0.002   PHE L  71 
 TRP   0.042   0.003   TRP H  55 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3432)
  covalent geometry    : angle       0.86585 ( 4673)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.81111 (    6)
  hydrogen bonds       : bond        0.03480 (   98)
  hydrogen bonds       : angle       5.39866 (  255)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8393 (t)
REVERT: A  408 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8537 (ptm-80)
REVERT: A  409 GLN cc_start: 0.8960 (mt0) cc_final: 0.8666 (tt0)
REVERT: A  442 ASP cc_start: 0.8668 (m-30) cc_final: 0.8349 (m-30)
REVERT: A  454 ARG cc_start: 0.9143 (ttm-80) cc_final: 0.8889 (ttm-80)
REVERT: H   81 VAL cc_start: 0.9228 (m) cc_final: 0.8925 (p)
REVERT: L   55 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8527 (tm-30)
REVERT: L   61 ARG cc_start: 0.8508 (ptt-90) cc_final: 0.8223 (ptp-170)
REVERT: L   81 GLU cc_start: 0.8682 (pm20) cc_final: 0.8226 (pm20)
REVERT: L   90 GLN cc_start: 0.9039 (pp30) cc_final: 0.8835 (pp30)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.3954
  time to fit residues: 58.1746
Evaluate side-chains
  141 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.087247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.075726 restraints weight = 7663.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.94
r_work: 0.3200 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   3435  Z= 0.239
  Angle     :  0.918  12.607   4679  Z= 0.438
  Chirality :  0.053   0.246    515
  Planarity :  0.006   0.060    598
  Dihedral  :  5.780  22.825    465
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 38.07 %
    Favored  : 58.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.41), residues: 422
  helix: -2.01 (1.85), residues: 12
  sheet: -1.01 (0.47), residues: 126
  loop : -0.87 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG L  61 
 TYR   0.032   0.002   TYR A 380 
 PHE   0.023   0.002   PHE H  24 
 TRP   0.059   0.004   TRP H  55 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 3432)
  covalent geometry    : angle       0.91835 ( 4673)
  SS BOND              : bond        0.00476 (    3)
  SS BOND              : angle       1.01216 (    6)
  hydrogen bonds       : bond        0.03584 (   98)
  hydrogen bonds       : angle       5.63169 (  255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.37 seconds
wall clock time: 34 minutes 38.62 seconds (2078.62 seconds total)