Starting phenix.real_space_refine
on Wed Jun  4 15:28:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t01_25574/06_2025/7t01_25574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t01_25574/06_2025/7t01_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_25574/06_2025/7t01_25574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t01_25574/06_2025/7t01_25574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t01_25574/06_2025/7t01_25574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t01_25574/06_2025/7t01_25574.cif"
  }
  resolution = 2.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.83, per 1000 atoms: 1.74
  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: 0.89
  Conformation dependent library (CDL) restraints added in 397.5 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: 0.55
  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: 1.15

  Time building geometry restraints manager: 1.05 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.310
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     17.560
  Find NCS groups from input model:        0.040
  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:16.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.750
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.025   0.002   TRP A 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.020   0.002   PHE L  83 
 TYR   0.047   0.005   TYR L  49 
 ARG   0.017   0.003   ARG H  60 

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

*********************** 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  : 0.399 
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: 0.7937
  time to fit residues: 139.2546
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  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 31 optimal weight:    0.1980
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.3180

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.091959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.079673 restraints weight = 7163.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.88
r_work: 0.3242 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3435  Z= 0.170
  Angle     :  0.771  10.090   4679  Z= 0.381
  Chirality :  0.049   0.188    515
  Planarity :  0.004   0.031    598
  Dihedral  :  6.517  23.971    465
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.84 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.37), residues: 422
  helix: -2.20 (1.29), residues: 18
  sheet: -0.12 (0.46), residues: 119
  loop : -0.73 (0.32), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 436 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.020   0.002   PHE L  83 
 TYR   0.012   0.002   TYR L  49 
 ARG   0.005   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (   98)
  hydrogen bonds       : angle       6.30592 (  255)
  SS BOND              : bond        0.00335 (    3)
  SS BOND              : angle       0.87725 (    6)
  covalent geometry    : bond        0.00392 ( 3432)
  covalent geometry    : angle       0.77116 ( 4673)

*********************** 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
  167 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 VAL cc_start: 0.8717 (t) cc_final: 0.8493 (p)
REVERT: A  425 LEU cc_start: 0.8942 (mt) cc_final: 0.8686 (mt)
REVERT: A  442 ASP cc_start: 0.8482 (m-30) cc_final: 0.8158 (m-30)
REVERT: A  454 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8772 (ttm110)
REVERT: A  456 PHE cc_start: 0.7943 (m-80) cc_final: 0.7692 (m-80)
REVERT: A  489 TYR cc_start: 0.7892 (m-80) cc_final: 0.7654 (m-10)
REVERT: H   24 PHE cc_start: 0.8851 (p90) cc_final: 0.8651 (p90)
REVERT: H   27 PHE cc_start: 0.8728 (p90) cc_final: 0.8458 (p90)
REVERT: H   61 TYR cc_start: 0.9069 (m-80) cc_final: 0.8822 (m-80)
REVERT: L    3 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7790 (mm-40)
REVERT: L   18 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7986 (ttm170)
REVERT: L   55 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8569 (tm-30)
REVERT: L   61 ARG cc_start: 0.8815 (ptt-90) cc_final: 0.8597 (ptt-90)
REVERT: L   86 TYR cc_start: 0.8440 (m-80) cc_final: 0.8220 (m-10)
  outliers start: 11
  outliers final: 3
  residues processed: 157
  average time/residue: 0.7789
  time to fit residues: 127.1917
Evaluate side-chains
  142 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain L residue    3 GLN
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   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 27 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.088175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.076355 restraints weight = 7295.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.81
r_work: 0.3206 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3435  Z= 0.246
  Angle     :  0.776  10.683   4679  Z= 0.389
  Chirality :  0.051   0.204    515
  Planarity :  0.005   0.041    598
  Dihedral  :  6.319  23.762    465
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 24.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.38), residues: 422
  helix: -2.38 (1.24), residues: 18
  sheet: -0.49 (0.46), residues: 121
  loop : -0.76 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  55 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.018   0.002   PHE H  96 
 TYR   0.014   0.002   TYR A 421 
 ARG   0.003   0.001   ARG H  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (   98)
  hydrogen bonds       : angle       5.87407 (  255)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       0.58493 (    6)
  covalent geometry    : bond        0.00564 ( 3432)
  covalent geometry    : angle       0.77660 ( 4673)

*********************** 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
  169 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8517 (ptm-80)
REVERT: A  421 TYR cc_start: 0.8669 (m-10) cc_final: 0.8413 (m-10)
REVERT: A  442 ASP cc_start: 0.8655 (m-30) cc_final: 0.8343 (m-30)
REVERT: A  454 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8757 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8045 (m-80) cc_final: 0.7810 (m-80)
REVERT: A  489 TYR cc_start: 0.7969 (m-80) cc_final: 0.7706 (m-10)
REVERT: H  119 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (p)
REVERT: L   55 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8654 (tm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 154
  average time/residue: 0.8303
  time to fit residues: 132.6118
Evaluate side-chains
  144 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   55 GLN
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 8 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 18 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 2 optimal weight:    0.2980
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.3780

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.088670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.077201 restraints weight = 7471.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.83
r_work: 0.3215 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3435  Z= 0.180
  Angle     :  0.761  12.080   4679  Z= 0.372
  Chirality :  0.049   0.190    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.988  23.281    465
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.39), residues: 422
  helix: -2.45 (1.24), residues: 18
  sheet: -0.59 (0.46), residues: 124
  loop : -0.79 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H  55 
 HIS   0.006   0.002   HIS H  99 
 PHE   0.038   0.002   PHE H  27 
 TYR   0.012   0.002   TYR L  87 
 ARG   0.006   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (   98)
  hydrogen bonds       : angle       5.66803 (  255)
  SS BOND              : bond        0.00452 (    3)
  SS BOND              : angle       0.35897 (    6)
  covalent geometry    : bond        0.00415 ( 3432)
  covalent geometry    : angle       0.76091 ( 4673)

*********************** 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
  163 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.8847 (mm) cc_final: 0.8638 (mp)
REVERT: A  408 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8556 (ptm-80)
REVERT: A  442 ASP cc_start: 0.8630 (m-30) cc_final: 0.8311 (m-30)
REVERT: A  454 ARG cc_start: 0.9172 (ttm-80) cc_final: 0.8789 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8008 (m-80) cc_final: 0.7783 (m-10)
REVERT: L   18 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8573 (ptm160)
REVERT: L   27 GLN cc_start: 0.7726 (mp10) cc_final: 0.7406 (mp10)
REVERT: L   55 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8645 (tm-30)
REVERT: L   75 ILE cc_start: 0.8722 (mp) cc_final: 0.8456 (tp)
  outliers start: 19
  outliers final: 9
  residues processed: 150
  average time/residue: 0.8450
  time to fit residues: 131.6258
Evaluate side-chains
  158 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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  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 L residue   18 ARG
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 35 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 1 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
L  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.088894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.077026 restraints weight = 7369.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.88
r_work: 0.3217 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
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 = 0.49   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 = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3435  Z= 0.187
  Angle     :  0.775  10.714   4679  Z= 0.378
  Chirality :  0.049   0.189    515
  Planarity :  0.005   0.042    598
  Dihedral  :  5.781  22.738    465
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 29.76 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.39), residues: 422
  helix: -2.58 (1.19), residues: 19
  sheet: -0.59 (0.47), residues: 124
  loop : -0.83 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H  55 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.036   0.002   PHE H  27 
 TYR   0.019   0.002   TYR A 380 
 ARG   0.003   0.000   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (   98)
  hydrogen bonds       : angle       5.46785 (  255)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       1.01933 (    6)
  covalent geometry    : bond        0.00433 ( 3432)
  covalent geometry    : angle       0.77508 ( 4673)

*********************** 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
  183 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8413 (t)
REVERT: A  355 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7359 (ttp-170)
REVERT: A  392 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8857 (m-80)
REVERT: A  408 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8571 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9060 (mt0) cc_final: 0.8739 (tt0)
REVERT: A  421 TYR cc_start: 0.8673 (m-10) cc_final: 0.8173 (m-80)
REVERT: A  442 ASP cc_start: 0.8652 (m-30) cc_final: 0.8324 (m-30)
REVERT: A  454 ARG cc_start: 0.9165 (ttm-80) cc_final: 0.8793 (ttm-80)
REVERT: A  456 PHE cc_start: 0.7970 (m-80) cc_final: 0.7725 (m-10)
REVERT: L   18 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8545 (ptm160)
REVERT: L   55 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8694 (tm-30)
REVERT: L   90 GLN cc_start: 0.8904 (pp30) cc_final: 0.8653 (pp30)
  outliers start: 24
  outliers final: 11
  residues processed: 164
  average time/residue: 0.7950
  time to fit residues: 135.5522
Evaluate side-chains
  168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
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  355 ARG
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
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   81 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 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 24 optimal weight:    0.0470
   chunk 30 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.088768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076879 restraints weight = 7568.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.93
r_work: 0.3217 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3435  Z= 0.194
  Angle     :  0.788  11.986   4679  Z= 0.382
  Chirality :  0.049   0.188    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.720  23.185    465
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 32.71 %
    Favored  : 61.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.40), residues: 422
  helix: -2.63 (1.20), residues: 19
  sheet: -0.67 (0.47), residues: 127
  loop : -0.79 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP H  55 
 HIS   0.001   0.000   HIS H  99 
 PHE   0.029   0.002   PHE H  27 
 TYR   0.024   0.002   TYR A 380 
 ARG   0.006   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03031 (   98)
  hydrogen bonds       : angle       5.51238 (  255)
  SS BOND              : bond        0.00369 (    3)
  SS BOND              : angle       0.67701 (    6)
  covalent geometry    : bond        0.00452 ( 3432)
  covalent geometry    : angle       0.78830 ( 4673)

*********************** 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
  172 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8420 (t)
REVERT: A  390 LEU cc_start: 0.8868 (mm) cc_final: 0.8658 (mp)
REVERT: A  392 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8872 (m-80)
REVERT: A  408 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8569 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9043 (mt0) cc_final: 0.8715 (tt0)
REVERT: A  421 TYR cc_start: 0.8661 (m-10) cc_final: 0.8272 (m-80)
REVERT: A  442 ASP cc_start: 0.8675 (m-30) cc_final: 0.8341 (m-30)
REVERT: A  454 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8928 (ttm-80)
REVERT: A  456 PHE cc_start: 0.7973 (m-80) cc_final: 0.7734 (m-80)
REVERT: L   18 ARG cc_start: 0.8721 (ttm170) cc_final: 0.8484 (ptm160)
REVERT: L   55 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8643 (tm-30)
REVERT: L   71 PHE cc_start: 0.8313 (m-80) cc_final: 0.8104 (m-80)
REVERT: L   90 GLN cc_start: 0.8947 (pp30) cc_final: 0.8718 (pp30)
  outliers start: 21
  outliers final: 11
  residues processed: 157
  average time/residue: 0.8166
  time to fit residues: 133.0804
Evaluate side-chains
  164 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  392 PHE
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   81 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 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:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 35 optimal weight:    0.2980
   chunk 41 optimal weight:    0.1980
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.2918

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.089958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.077925 restraints weight = 7390.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.92
r_work: 0.3235 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3435  Z= 0.156
  Angle     :  0.797  12.491   4679  Z= 0.380
  Chirality :  0.048   0.179    515
  Planarity :  0.005   0.043    598
  Dihedral  :  5.585  22.540    465
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 34.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.40), residues: 422
  helix: -2.63 (1.22), residues: 19
  sheet: -0.74 (0.47), residues: 128
  loop : -0.82 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP H  55 
 HIS   0.001   0.000   HIS H  99 
 PHE   0.026   0.002   PHE H  27 
 TYR   0.012   0.001   TYR L  36 
 ARG   0.009   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (   98)
  hydrogen bonds       : angle       5.33009 (  255)
  SS BOND              : bond        0.00404 (    3)
  SS BOND              : angle       0.94310 (    6)
  covalent geometry    : bond        0.00365 ( 3432)
  covalent geometry    : angle       0.79708 ( 4673)

*********************** 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
  173 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8412 (t)
REVERT: A  355 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8359 (tpp-160)
REVERT: A  390 LEU cc_start: 0.8862 (mm) cc_final: 0.8636 (mp)
REVERT: A  392 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (m-80)
REVERT: A  408 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8592 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9007 (mt0) cc_final: 0.8693 (tt0)
REVERT: A  421 TYR cc_start: 0.8696 (m-10) cc_final: 0.8347 (m-80)
REVERT: A  442 ASP cc_start: 0.8657 (m-30) cc_final: 0.8331 (m-30)
REVERT: A  454 ARG cc_start: 0.9151 (ttm-80) cc_final: 0.8939 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8011 (m-80) cc_final: 0.7750 (m-80)
REVERT: A  516 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7029 (tm-30)
REVERT: L    3 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8224 (mm110)
REVERT: L   18 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (ptm160)
REVERT: L   55 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8584 (tm-30)
REVERT: L   75 ILE cc_start: 0.8758 (mp) cc_final: 0.8449 (tp)
REVERT: L   90 GLN cc_start: 0.8900 (pp30) cc_final: 0.8665 (pp30)
  outliers start: 17
  outliers final: 5
  residues processed: 161
  average time/residue: 0.7744
  time to fit residues: 129.5493
Evaluate side-chains
  159 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  392 PHE
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   81 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 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 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.086842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.075372 restraints weight = 7440.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.85
r_work: 0.3189 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   3435  Z= 0.267
  Angle     :  0.849  12.290   4679  Z= 0.412
  Chirality :  0.052   0.201    515
  Planarity :  0.006   0.056    598
  Dihedral  :  5.873  23.853    465
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 35.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.40), residues: 422
  helix: -2.70 (1.16), residues: 19
  sheet: -0.49 (0.48), residues: 120
  loop : -1.00 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP H  55 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.023   0.002   PHE H  24 
 TYR   0.021   0.002   TYR A 380 
 ARG   0.012   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (   98)
  hydrogen bonds       : angle       5.46772 (  255)
  SS BOND              : bond        0.00440 (    3)
  SS BOND              : angle       1.23191 (    6)
  covalent geometry    : bond        0.00613 ( 3432)
  covalent geometry    : angle       0.84859 ( 4673)

*********************** 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
  165 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8455 (t)
REVERT: A  392 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8844 (m-80)
REVERT: A  408 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8567 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9061 (mt0) cc_final: 0.8787 (tt0)
REVERT: A  421 TYR cc_start: 0.8716 (m-10) cc_final: 0.8413 (m-80)
REVERT: A  442 ASP cc_start: 0.8703 (m-30) cc_final: 0.8401 (m-30)
REVERT: A  454 ARG cc_start: 0.9186 (ttm-80) cc_final: 0.8945 (ttm-80)
REVERT: L   18 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8498 (ptm160)
REVERT: L   55 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8667 (tm-30)
REVERT: L   75 ILE cc_start: 0.8733 (mp) cc_final: 0.8443 (tp)
REVERT: L   90 GLN cc_start: 0.9029 (pp30) cc_final: 0.8816 (pp30)
  outliers start: 17
  outliers final: 8
  residues processed: 153
  average time/residue: 0.8931
  time to fit residues: 141.4445
Evaluate side-chains
  159 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   32 ILE
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   60 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 11 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0570
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.088247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.076588 restraints weight = 7460.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.89
r_work: 0.3214 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    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 = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3435  Z= 0.209
  Angle     :  0.893  12.930   4679  Z= 0.431
  Chirality :  0.051   0.190    515
  Planarity :  0.006   0.064    598
  Dihedral  :  5.760  23.458    465
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 38.07 %
    Favored  : 57.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.41), residues: 422
  helix: -2.79 (1.13), residues: 19
  sheet: -0.69 (0.47), residues: 127
  loop : -0.97 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.004   TRP H  55 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.025   0.003   PHE H  24 
 TYR   0.033   0.002   TYR A 473 
 ARG   0.013   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (   98)
  hydrogen bonds       : angle       5.50326 (  255)
  SS BOND              : bond        0.00587 (    3)
  SS BOND              : angle       1.68091 (    6)
  covalent geometry    : bond        0.00490 ( 3432)
  covalent geometry    : angle       0.89113 ( 4673)

*********************** 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
  160 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8465 (t)
REVERT: A  392 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8808 (m-80)
REVERT: A  408 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9050 (mt0) cc_final: 0.8757 (tt0)
REVERT: A  421 TYR cc_start: 0.8685 (m-10) cc_final: 0.8351 (m-80)
REVERT: A  442 ASP cc_start: 0.8658 (m-30) cc_final: 0.8337 (m-30)
REVERT: A  454 ARG cc_start: 0.9116 (ttm-80) cc_final: 0.8897 (ttm-80)
REVERT: L    3 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8038 (mm110)
REVERT: L   18 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8469 (ptm160)
REVERT: L   55 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8582 (tm-30)
REVERT: L   71 PHE cc_start: 0.8283 (m-80) cc_final: 0.8079 (m-80)
REVERT: L   90 GLN cc_start: 0.9011 (pp30) cc_final: 0.8806 (pp30)
  outliers start: 15
  outliers final: 9
  residues processed: 151
  average time/residue: 0.8323
  time to fit residues: 130.4734
Evaluate side-chains
  155 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  392 PHE
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   25 SER
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue    5 THR
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   60 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0870
   chunk 35 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0870
   chunk 15 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.1492

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

Flipped N/Q/H residues before XYZ refinement:
** L  79 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 = 0.3564 r_free = 0.3564 target = 0.090288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.078573 restraints weight = 7407.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.95
r_work: 0.3254 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.4604

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= 0.149
  Angle     :  0.878  13.207   4679  Z= 0.422
  Chirality :  0.050   0.174    515
  Planarity :  0.006   0.052    598
  Dihedral  :  5.599  25.577    465
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 37.53 %
    Favored  : 57.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.40), residues: 422
  helix: -2.86 (1.12), residues: 19
  sheet: -0.82 (0.46), residues: 127
  loop : -0.94 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP H  38 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.025   0.002   PHE H  27 
 TYR   0.035   0.002   TYR A 473 
 ARG   0.013   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (   98)
  hydrogen bonds       : angle       5.48942 (  255)
  SS BOND              : bond        0.00415 (    3)
  SS BOND              : angle       1.45457 (    6)
  covalent geometry    : bond        0.00364 ( 3432)
  covalent geometry    : angle       0.87653 ( 4673)

********************** 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
  164 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8432 (t)
REVERT: A  355 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8349 (tpp-160)
REVERT: A  392 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8767 (m-80)
REVERT: A  408 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8547 (ptm-80)
REVERT: A  409 GLN cc_start: 0.8981 (mt0) cc_final: 0.8704 (tt0)
REVERT: A  421 TYR cc_start: 0.8627 (m-10) cc_final: 0.8287 (m-80)
REVERT: A  442 ASP cc_start: 0.8626 (m-30) cc_final: 0.8316 (m-30)
REVERT: A  454 ARG cc_start: 0.9070 (ttm-80) cc_final: 0.8783 (ttm-80)
REVERT: L    3 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8103 (mm110)
REVERT: L   10 SER cc_start: 0.8748 (t) cc_final: 0.8416 (p)
REVERT: L   55 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8450 (tm-30)
REVERT: L   61 ARG cc_start: 0.8634 (ptt-90) cc_final: 0.8345 (ptp-170)
REVERT: L   79 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8070 (mm-40)
REVERT: L   81 GLU cc_start: 0.8618 (pm20) cc_final: 0.7789 (pp20)
REVERT: L   90 GLN cc_start: 0.8983 (pp30) cc_final: 0.8750 (pp30)
  outliers start: 17
  outliers final: 7
  residues processed: 150
  average time/residue: 0.8470
  time to fit residues: 131.7332
Evaluate side-chains
  153 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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  392 PHE
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   25 SER
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   75 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0010
   chunk 37 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0170
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   overall best weight:    0.1800

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

Flipped N/Q/H residues before XYZ refinement:
** L  79 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 = 0.3578 r_free = 0.3578 target = 0.091089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.079423 restraints weight = 7341.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.94
r_work: 0.3266 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3435  Z= 0.159
  Angle     :  0.919  12.794   4679  Z= 0.434
  Chirality :  0.051   0.278    515
  Planarity :  0.005   0.047    598
  Dihedral  :  5.490  24.089    465
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 38.87 %
    Favored  : 57.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.42), residues: 422
  helix: -2.75 (1.14), residues: 19
  sheet: -0.82 (0.47), residues: 126
  loop : -0.76 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP H  55 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.023   0.002   PHE H  27 
 TYR   0.034   0.002   TYR A 473 
 ARG   0.011   0.001   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (   98)
  hydrogen bonds       : angle       5.39540 (  255)
  SS BOND              : bond        0.00535 (    3)
  SS BOND              : angle       1.27309 (    6)
  covalent geometry    : bond        0.00394 ( 3432)
  covalent geometry    : angle       0.91895 ( 4673)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3999.13 seconds
wall clock time: 68 minutes 55.87 seconds (4135.87 seconds total)