Starting phenix.real_space_refine
on Sat May  2 06:23:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yw2_73536/05_2026/9yw2_73536.map"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.010
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       9      5.16       5
     C    1644      2.51       5
     N     461      2.21       5
     O     496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2610
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1514
          Classifications: {'peptide': 191}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 11, 'TRANS': 179}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "H"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1025
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 112}
    Chain: "I"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 71
          Classifications: {'peptide': 10}
          Link IDs: {'TRANS': 9}
  Time building chain proxies: 0.80, per 1000 atoms: 0.31
  Number of scatterers: 2610
  At special positions: 0
  Unit cell: (74.2976, 66.1713, 104.481, 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       9     16.00
     O     496      8.00
     N     461      7.00
     C    1644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.17
  Conformation dependent library (CDL) restraints added in 89.6 milliseconds
  

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  614

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      27.9% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 50
      removed outlier: 3.909A  pdb=" N   ASP A  47 " --> pdb=" O   GLN A  43 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLU A  48 " --> pdb=" O   PRO A  44 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 92
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 134 through 140
    Processing helix  chain 'A' and resid 190 through 197
      removed outlier: 3.587A  pdb=" N   SER A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 530 through 557
      removed outlier: 4.554A  pdb=" N   GLN H 536 " --> pdb=" O   GLU H 532 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 558 through 561
      removed outlier: 3.587A  pdb=" N   LEU H 561 " --> pdb=" O   GLU H 558 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 558 through 561'
    Processing helix  chain 'H' and resid 596 through 605
      removed outlier: 3.755A  pdb=" N   PHE H 600 " --> pdb=" O   LEU H 596 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 623 through 627
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30
      removed outlier: 7.385A  pdb=" N   ILE A  82 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ILE A  27 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   MET A  84 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ASP A  29 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   LYS A  81 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   SER A  42 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154
      removed outlier: 6.820A  pdb=" N   HIS A 115 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   THR A 168 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ARG A 113 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE A 182 " --> pdb=" O   ASN I 233 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ASN I 233 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147
    Processing sheet with id=AA4, first strand: chain 'H' and resid 587 through 591
      removed outlier: 3.692A  pdb=" N   ARG H 588 " --> pdb=" O   LEU H 576 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   GLU H 642 " --> pdb=" O   VAL H 573 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS H 575 " --> pdb=" O   GLU H 642 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   LEU H 644 " --> pdb=" O   LYS H 575 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG H 577 " --> pdb=" O   LEU H 644 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   LEU H 646 " --> pdb=" O   ARG H 577 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ARG H 579 " --> pdb=" O   LEU H 646 " (cutoff:3.500A)
      removed outlier: 8.838A  pdb=" N   ALA H 648 " --> pdb=" O   ARG H 579 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLU H 647 " --> pdb=" O   LYS H 614 " (cutoff:3.500A)

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

  Time building geometry restraints manager: 0.25 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: 890
        1.34 -     1.46: 368
        1.46 -     1.57: 1381
        1.57 -     1.69: 1
        1.69 -     1.81: 13
  Bond restraints: 2653
  Sorted by residual:
  bond pdb=" CA  LYS A  18 "
       pdb=" CB  LYS A  18 "
    ideal  model  delta    sigma   weight residual
    1.528  1.594 -0.066 2.61e-02 1.47e+03 6.40e+00
  bond pdb=" CA  GLU A 196 "
       pdb=" C   GLU A 196 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.015 1.41e-02 5.03e+03 1.17e+00
  bond pdb=" CB  GLN H 546 "
       pdb=" CG  GLN H 546 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.98e-01
  bond pdb=" CB  ASP H 623 "
       pdb=" CG  ASP H 623 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.07e-01
  bond pdb=" CA  GLN H 546 "
       pdb=" CB  GLN H 546 "
    ideal  model  delta    sigma   weight residual
    1.528  1.544 -0.015 1.66e-02 3.63e+03 8.51e-01
  ... (remaining 2648 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 3411
        1.56 -     3.11: 133
        3.11 -     4.67: 22
        4.67 -     6.22: 7
        6.22 -     7.78: 3
  Bond angle restraints: 3576
  Sorted by residual:
  angle pdb=" CA  GLN H 546 "
        pdb=" CB  GLN H 546 "
        pdb=" CG  GLN H 546 "
      ideal   model   delta    sigma   weight residual
     114.10  121.88   -7.78 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" N   MET H 533 "
        pdb=" CA  MET H 533 "
        pdb=" C   MET H 533 "
      ideal   model   delta    sigma   weight residual
     113.88  110.33    3.55 1.23e+00 6.61e-01 8.32e+00
  angle pdb=" CA  GLU H 547 "
        pdb=" CB  GLU H 547 "
        pdb=" CG  GLU H 547 "
      ideal   model   delta    sigma   weight residual
     114.10  119.56   -5.46 2.00e+00 2.50e-01 7.45e+00
  angle pdb=" CA  GLN H 641 "
        pdb=" CB  GLN H 641 "
        pdb=" CG  GLN H 641 "
      ideal   model   delta    sigma   weight residual
     114.10  119.47   -5.37 2.00e+00 2.50e-01 7.21e+00
  angle pdb=" CA  LYS H 637 "
        pdb=" CB  LYS H 637 "
        pdb=" CG  LYS H 637 "
      ideal   model   delta    sigma   weight residual
     114.10  119.18   -5.08 2.00e+00 2.50e-01 6.44e+00
  ... (remaining 3571 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.85: 1390
       15.85 -    31.69: 207
       31.69 -    47.53: 57
       47.53 -    63.38: 10
       63.38 -    79.22: 3
  Dihedral angle restraints: 1667
    sinusoidal: 726
      harmonic: 941
  Sorted by residual:
  dihedral pdb=" CA  PRO H 640 "
           pdb=" C   PRO H 640 "
           pdb=" N   GLN H 641 "
           pdb=" CA  GLN H 641 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.95  -30.05     0      5.00e+00 4.00e-02 3.61e+01
  dihedral pdb=" CA  ASP A 169 "
           pdb=" C   ASP A 169 "
           pdb=" N   PRO A 170 "
           pdb=" CA  PRO A 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.81   20.19     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  LYS H 637 "
           pdb=" C   LYS H 637 "
           pdb=" N   LEU H 638 "
           pdb=" CA  LEU H 638 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.97   20.03     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 1664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 242
       0.033 -    0.066: 84
       0.066 -    0.098: 44
       0.098 -    0.131: 24
       0.131 -    0.164: 2
  Chirality restraints: 396
  Sorted by residual:
  chirality pdb=" CA  LYS H 637 "
            pdb=" N   LYS H 637 "
            pdb=" C   LYS H 637 "
            pdb=" CB  LYS H 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.73e-01
  chirality pdb=" CA  LYS A  18 "
            pdb=" N   LYS A  18 "
            pdb=" C   LYS A  18 "
            pdb=" CB  LYS A  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  ILE A  70 "
            pdb=" N   ILE A  70 "
            pdb=" C   ILE A  70 "
            pdb=" CB  ILE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 393 not shown)

  Planarity restraints: 475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 639 "   -0.043 5.00e-02 4.00e+02   6.47e-02 6.70e+00
        pdb=" N   PRO H 640 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO H 640 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO H 640 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR H 580 "   -0.028 5.00e-02 4.00e+02   4.24e-02 2.87e+00
        pdb=" N   PRO H 581 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO H 581 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO H 581 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 107 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.10e+00
        pdb=" C   ASP A 107 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A 107 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 108 "    0.008 2.00e-02 2.50e+03
  ... (remaining 472 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 391
        2.76 -     3.29: 2635
        3.29 -     3.83: 4086
        3.83 -     4.36: 4662
        4.36 -     4.90: 7817
  Nonbonded interactions: 19591
  Sorted by model distance:
  nonbonded pdb=" OG  SER H 605 "
            pdb=" NZ  LYS H 606 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OG1 THR A 168 "
            pdb=" O   PRO A 170 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ARG A  86 "
            pdb=" ND2 ASN A  90 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" N   ASP A 204 "
            pdb=" OD1 ASP A 204 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" NH1 ARG A 113 "
            pdb=" OD1 ASP A 169 "
     model   vdw
     2.330 3.120
  ... (remaining 19586 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:             1.490
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.240
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
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      :  0.003   0.066   2653  Z= 0.162
  Angle     :  0.761   7.779   3576  Z= 0.407
  Chirality :  0.047   0.164    396
  Planarity :  0.005   0.065    475
  Dihedral  : 16.096  79.224   1053
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  4.10 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 26.80 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.46), residues: 317
  helix: -0.08 (0.67), residues: 57
  sheet: -0.17 (0.58), residues: 72
  loop : -0.57 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  25 
 TYR   0.003   0.001   TYR A 203 
 PHE   0.021   0.002   PHE A  52 
 TRP   0.007   0.001   TRP H 610 
 HIS   0.003   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2653)
  covalent geometry    : angle       0.76087 ( 3576)
  hydrogen bonds       : bond        0.17580 (   79)
  hydrogen bonds       : angle       7.58460 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ARG cc_start: 0.6668 (mpt180) cc_final: 0.3882 (mpt180)
REVERT: A  126 ILE cc_start: 0.9022 (mm) cc_final: 0.8642 (mm)
REVERT: H  575 LYS cc_start: 0.9135 (tttt) cc_final: 0.8636 (tptm)
REVERT: H  596 LEU cc_start: 0.9455 (tp) cc_final: 0.9240 (tp)
REVERT: H  597 GLN cc_start: 0.9323 (tp-100) cc_final: 0.8966 (tp-100)
REVERT: H  598 ILE cc_start: 0.9425 (mm) cc_final: 0.9145 (mp)
REVERT: H  600 PHE cc_start: 0.9260 (m-80) cc_final: 0.8674 (m-80)
REVERT: H  601 ASP cc_start: 0.8931 (m-30) cc_final: 0.8300 (m-30)
REVERT: H  611 ASP cc_start: 0.9360 (p0) cc_final: 0.9004 (p0)
REVERT: H  614 LYS cc_start: 0.9265 (pttt) cc_final: 0.8832 (ptpp)
REVERT: H  626 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8824 (mm-40)
REVERT: H  628 ASP cc_start: 0.9210 (t0) cc_final: 0.8897 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0806
  time to fit residues: 9.2301
Evaluate side-chains
  91 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  169 ASP
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A  90 ASN
** H 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.141953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.094863 restraints weight = 4783.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 4.25
r_work: 0.3113 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   2653  Z= 0.192
  Angle     :  0.691   6.296   3576  Z= 0.359
  Chirality :  0.050   0.146    396
  Planarity :  0.006   0.061    475
  Dihedral  :  7.562  59.708    369
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  5.05 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 26.12 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.46), residues: 317
  helix: -0.22 (0.65), residues: 63
  sheet: -0.18 (0.55), residues: 80
  loop : -0.36 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H 622 
 TYR   0.005   0.001   TYR A 138 
 PHE   0.014   0.002   PHE A 139 
 TRP   0.009   0.002   TRP H 610 
 HIS   0.003   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 2653)
  covalent geometry    : angle       0.69103 ( 3576)
  hydrogen bonds       : bond        0.03924 (   79)
  hydrogen bonds       : angle       5.82892 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7383 (mmt180) cc_final: 0.6970 (mmp80)
REVERT: A   64 ARG cc_start: 0.6885 (mpt180) cc_final: 0.4571 (mpt180)
REVERT: A  126 ILE cc_start: 0.9138 (mm) cc_final: 0.8657 (mm)
REVERT: A  155 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8004 (mmm160)
REVERT: H  546 GLN cc_start: 0.8960 (pp30) cc_final: 0.8746 (pp30)
REVERT: H  575 LYS cc_start: 0.9116 (tttt) cc_final: 0.8486 (tptm)
REVERT: H  596 LEU cc_start: 0.9413 (tp) cc_final: 0.9098 (tp)
REVERT: H  597 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9037 (tp-100)
REVERT: H  600 PHE cc_start: 0.9408 (m-80) cc_final: 0.8687 (m-80)
REVERT: H  601 ASP cc_start: 0.9127 (m-30) cc_final: 0.8519 (m-30)
REVERT: H  606 LYS cc_start: 0.8807 (mptt) cc_final: 0.8552 (mptt)
REVERT: H  611 ASP cc_start: 0.9394 (p0) cc_final: 0.9045 (p0)
REVERT: H  614 LYS cc_start: 0.9087 (pttt) cc_final: 0.8618 (ptpp)
REVERT: H  626 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8726 (mm-40)
REVERT: H  628 ASP cc_start: 0.9072 (t0) cc_final: 0.8704 (t0)
REVERT: H  632 SER cc_start: 0.8902 (p) cc_final: 0.8679 (t)
REVERT: H  647 GLU cc_start: 0.8882 (tp30) cc_final: 0.8657 (tp30)
REVERT: I  234 ARG cc_start: 0.8527 (mtm110) cc_final: 0.8306 (mtm110)
  outliers start: 15
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0763
  time to fit residues: 8.0346
Evaluate side-chains
  86 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  169 ASP
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 569 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.142038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.095553 restraints weight = 4778.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 4.18
r_work: 0.3129 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2653  Z= 0.151
  Angle     :  0.666   7.278   3576  Z= 0.340
  Chirality :  0.049   0.140    396
  Planarity :  0.005   0.060    475
  Dihedral  :  7.044  53.703    365
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  4.42 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 24.40 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.46), residues: 317
  helix: -0.25 (0.63), residues: 63
  sheet: -0.25 (0.55), residues: 80
  loop : -0.33 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  25 
 TYR   0.017   0.001   TYR A 134 
 PHE   0.017   0.002   PHE H 608 
 TRP   0.011   0.002   TRP H 610 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2653)
  covalent geometry    : angle       0.66567 ( 3576)
  hydrogen bonds       : bond        0.03464 (   79)
  hydrogen bonds       : angle       5.55029 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7324 (mmt180) cc_final: 0.6996 (mmp80)
REVERT: A   26 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8470 (mm)
REVERT: A   35 ASP cc_start: 0.8669 (t0) cc_final: 0.8324 (t0)
REVERT: A   64 ARG cc_start: 0.6839 (mpt180) cc_final: 0.4423 (mpt180)
REVERT: A  155 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7717 (tmt-80)
REVERT: A  158 MET cc_start: 0.8862 (pmm) cc_final: 0.8624 (pmm)
REVERT: H  575 LYS cc_start: 0.9147 (tttt) cc_final: 0.8570 (tptm)
REVERT: H  594 ASN cc_start: 0.7319 (t0) cc_final: 0.6982 (t0)
REVERT: H  595 LYS cc_start: 0.8781 (tttt) cc_final: 0.8510 (tmmt)
REVERT: H  596 LEU cc_start: 0.9554 (tp) cc_final: 0.9267 (tp)
REVERT: H  597 GLN cc_start: 0.9417 (tp-100) cc_final: 0.9124 (tp-100)
REVERT: H  598 ILE cc_start: 0.9386 (mm) cc_final: 0.9132 (mp)
REVERT: H  600 PHE cc_start: 0.9412 (m-80) cc_final: 0.8700 (m-80)
REVERT: H  601 ASP cc_start: 0.9121 (m-30) cc_final: 0.8493 (m-30)
REVERT: H  606 LYS cc_start: 0.8640 (mptt) cc_final: 0.8410 (mptt)
REVERT: H  611 ASP cc_start: 0.9367 (p0) cc_final: 0.8993 (p0)
REVERT: H  614 LYS cc_start: 0.9179 (pttt) cc_final: 0.8731 (ptpp)
REVERT: H  626 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8722 (mm-40)
REVERT: H  628 ASP cc_start: 0.9031 (t0) cc_final: 0.8647 (t0)
REVERT: H  632 SER cc_start: 0.8884 (p) cc_final: 0.8664 (t)
REVERT: I  234 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8292 (mtm110)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0841
  time to fit residues: 8.6363
Evaluate side-chains
  83 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  580 THR
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 14 optimal weight:    0.0010
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.143297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.095769 restraints weight = 4699.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 4.24
r_work: 0.3127 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2653  Z= 0.138
  Angle     :  0.639   6.427   3576  Z= 0.331
  Chirality :  0.048   0.138    396
  Planarity :  0.005   0.060    475
  Dihedral  :  6.053  49.005    360
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.05 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 22.34 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.46), residues: 317
  helix: -0.17 (0.65), residues: 63
  sheet: -0.35 (0.59), residues: 72
  loop : -0.49 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 622 
 TYR   0.003   0.001   TYR A 138 
 PHE   0.010   0.002   PHE H 602 
 TRP   0.011   0.002   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2653)
  covalent geometry    : angle       0.63863 ( 3576)
  hydrogen bonds       : bond        0.03364 (   79)
  hydrogen bonds       : angle       5.38413 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7275 (mmt180) cc_final: 0.7006 (mmp80)
REVERT: A   26 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8466 (mm)
REVERT: A   64 ARG cc_start: 0.6928 (mpt180) cc_final: 0.4601 (mpt180)
REVERT: H  575 LYS cc_start: 0.9137 (tttt) cc_final: 0.8557 (tptm)
REVERT: H  596 LEU cc_start: 0.9380 (tp) cc_final: 0.9088 (tp)
REVERT: H  597 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9089 (tp-100)
REVERT: H  598 ILE cc_start: 0.9342 (mm) cc_final: 0.9135 (mp)
REVERT: H  600 PHE cc_start: 0.9399 (m-80) cc_final: 0.8637 (m-80)
REVERT: H  601 ASP cc_start: 0.9121 (m-30) cc_final: 0.8497 (m-30)
REVERT: H  606 LYS cc_start: 0.8585 (mptt) cc_final: 0.8319 (mptt)
REVERT: H  611 ASP cc_start: 0.9366 (p0) cc_final: 0.8979 (p0)
REVERT: H  614 LYS cc_start: 0.9179 (pttt) cc_final: 0.8745 (ptpp)
REVERT: H  626 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8743 (mm-40)
REVERT: H  628 ASP cc_start: 0.8983 (t0) cc_final: 0.8601 (t0)
REVERT: H  632 SER cc_start: 0.8876 (p) cc_final: 0.8665 (t)
REVERT: H  642 GLU cc_start: 0.8245 (pp20) cc_final: 0.7622 (pp20)
REVERT: I  234 ARG cc_start: 0.8572 (mtm110) cc_final: 0.8300 (mtm110)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0819
  time to fit residues: 8.8380
Evaluate side-chains
  88 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  580 THR
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0670
   overall best weight:    0.7518

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A  50 GLN
** H 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.142357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.095479 restraints weight = 4676.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 4.09
r_work: 0.3114 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2653  Z= 0.172
  Angle     :  0.656   7.486   3576  Z= 0.340
  Chirality :  0.049   0.137    396
  Planarity :  0.005   0.058    475
  Dihedral  :  5.475  42.816    358
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.68 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 24.05 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.46), residues: 317
  helix: -0.32 (0.64), residues: 63
  sheet: -0.42 (0.57), residues: 79
  loop : -0.55 (0.46), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 588 
 TYR   0.019   0.001   TYR A 134 
 PHE   0.009   0.002   PHE H 602 
 TRP   0.008   0.002   TRP H 610 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 2653)
  covalent geometry    : angle       0.65603 ( 3576)
  hydrogen bonds       : bond        0.03217 (   79)
  hydrogen bonds       : angle       5.35974 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7299 (mmt180) cc_final: 0.7071 (mmp80)
REVERT: A   64 ARG cc_start: 0.7005 (mpt180) cc_final: 0.4549 (mpt180)
REVERT: A  199 ASN cc_start: 0.7278 (p0) cc_final: 0.6721 (p0)
REVERT: H  575 LYS cc_start: 0.9187 (tttt) cc_final: 0.8600 (tptm)
REVERT: H  594 ASN cc_start: 0.7590 (t0) cc_final: 0.7230 (t0)
REVERT: H  596 LEU cc_start: 0.9551 (tp) cc_final: 0.9297 (tt)
REVERT: H  597 GLN cc_start: 0.9446 (tp-100) cc_final: 0.9143 (tp-100)
REVERT: H  598 ILE cc_start: 0.9423 (mm) cc_final: 0.9184 (mp)
REVERT: H  601 ASP cc_start: 0.9095 (m-30) cc_final: 0.8500 (m-30)
REVERT: H  606 LYS cc_start: 0.8610 (mptt) cc_final: 0.8362 (mptt)
REVERT: H  611 ASP cc_start: 0.9363 (p0) cc_final: 0.9022 (p0)
REVERT: H  614 LYS cc_start: 0.9224 (pttt) cc_final: 0.8782 (ptpp)
REVERT: H  626 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8739 (mm-40)
REVERT: H  628 ASP cc_start: 0.8946 (t0) cc_final: 0.8589 (t0)
REVERT: H  632 SER cc_start: 0.8877 (p) cc_final: 0.8655 (t)
REVERT: H  642 GLU cc_start: 0.8252 (pp20) cc_final: 0.7689 (pp20)
REVERT: I  234 ARG cc_start: 0.8598 (mtm110) cc_final: 0.8371 (mtm110)
  outliers start: 15
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0786
  time to fit residues: 7.5420
Evaluate side-chains
  87 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  580 THR
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.141073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.093912 restraints weight = 4727.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 4.08
r_work: 0.3087 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2653  Z= 0.203
  Angle     :  0.663   6.767   3576  Z= 0.344
  Chirality :  0.050   0.137    396
  Planarity :  0.005   0.059    475
  Dihedral  :  5.548  42.528    358
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.68 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 26.46 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.46), residues: 317
  helix: -0.18 (0.66), residues: 63
  sheet: -0.53 (0.57), residues: 79
  loop : -0.64 (0.46), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 588 
 TYR   0.015   0.001   TYR A 134 
 PHE   0.011   0.002   PHE H 608 
 TRP   0.013   0.003   TRP H 610 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 2653)
  covalent geometry    : angle       0.66313 ( 3576)
  hydrogen bonds       : bond        0.03387 (   79)
  hydrogen bonds       : angle       5.37802 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ARG cc_start: 0.7009 (mpt180) cc_final: 0.4492 (mtt90)
REVERT: H  546 GLN cc_start: 0.8904 (pp30) cc_final: 0.8341 (pp30)
REVERT: H  575 LYS cc_start: 0.9173 (tttt) cc_final: 0.8589 (tptm)
REVERT: H  594 ASN cc_start: 0.7649 (t0) cc_final: 0.7275 (t0)
REVERT: H  596 LEU cc_start: 0.9422 (tp) cc_final: 0.9118 (tp)
REVERT: H  597 GLN cc_start: 0.9402 (tp-100) cc_final: 0.9090 (tp-100)
REVERT: H  598 ILE cc_start: 0.9389 (mm) cc_final: 0.9175 (mp)
REVERT: H  600 PHE cc_start: 0.9415 (m-80) cc_final: 0.8599 (m-80)
REVERT: H  601 ASP cc_start: 0.9105 (m-30) cc_final: 0.8505 (m-30)
REVERT: H  606 LYS cc_start: 0.8620 (mptt) cc_final: 0.8388 (mptt)
REVERT: H  611 ASP cc_start: 0.9366 (p0) cc_final: 0.8990 (p0)
REVERT: H  614 LYS cc_start: 0.9224 (pttt) cc_final: 0.8828 (ptpp)
REVERT: H  626 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8752 (mm-40)
REVERT: H  628 ASP cc_start: 0.8912 (t0) cc_final: 0.8462 (t0)
REVERT: H  632 SER cc_start: 0.8893 (p) cc_final: 0.8683 (t)
REVERT: H  642 GLU cc_start: 0.8227 (pp20) cc_final: 0.7607 (pp20)
REVERT: I  234 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8379 (mtm110)
  outliers start: 14
  outliers final: 14
  residues processed: 81
  average time/residue: 0.0792
  time to fit residues: 7.4114
Evaluate side-chains
  86 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  580 THR
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.141378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.094699 restraints weight = 4686.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 4.06
r_work: 0.3100 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2653  Z= 0.167
  Angle     :  0.657   7.051   3576  Z= 0.339
  Chirality :  0.048   0.140    396
  Planarity :  0.005   0.058    475
  Dihedral  :  5.387  40.962    358
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.36 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 27.49 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.46), residues: 317
  helix: -0.31 (0.64), residues: 63
  sheet: -0.56 (0.58), residues: 78
  loop : -0.50 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 588 
 TYR   0.015   0.001   TYR A 134 
 PHE   0.010   0.002   PHE H 608 
 TRP   0.011   0.003   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 2653)
  covalent geometry    : angle       0.65682 ( 3576)
  hydrogen bonds       : bond        0.03182 (   79)
  hydrogen bonds       : angle       5.33007 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ARG cc_start: 0.7099 (mpt180) cc_final: 0.4542 (mpt180)
REVERT: H  575 LYS cc_start: 0.9173 (tttt) cc_final: 0.8593 (tptm)
REVERT: H  596 LEU cc_start: 0.9558 (tp) cc_final: 0.9297 (tt)
REVERT: H  597 GLN cc_start: 0.9418 (tp-100) cc_final: 0.9102 (tp-100)
REVERT: H  598 ILE cc_start: 0.9476 (mm) cc_final: 0.9206 (mp)
REVERT: H  601 ASP cc_start: 0.9056 (m-30) cc_final: 0.8443 (m-30)
REVERT: H  606 LYS cc_start: 0.8614 (mptt) cc_final: 0.8358 (mptt)
REVERT: H  611 ASP cc_start: 0.9359 (p0) cc_final: 0.8989 (p0)
REVERT: H  614 LYS cc_start: 0.9336 (pttt) cc_final: 0.8915 (ptpp)
REVERT: H  626 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8758 (mm-40)
REVERT: H  628 ASP cc_start: 0.9013 (t0) cc_final: 0.8662 (t0)
REVERT: H  632 SER cc_start: 0.8936 (p) cc_final: 0.8692 (t)
REVERT: H  633 LEU cc_start: 0.9623 (mm) cc_final: 0.9275 (mm)
REVERT: H  642 GLU cc_start: 0.8218 (pp20) cc_final: 0.7608 (pp20)
REVERT: I  234 ARG cc_start: 0.8644 (mtm110) cc_final: 0.8373 (mtm110)
  outliers start: 16
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0841
  time to fit residues: 8.1422
Evaluate side-chains
  88 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  580 THR
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0270
   chunk 31 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
** H 546 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 = 0.3990 r_free = 0.3990 target = 0.142919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.095780 restraints weight = 4799.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 4.16
r_work: 0.3117 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2653  Z= 0.135
  Angle     :  0.651   7.771   3576  Z= 0.338
  Chirality :  0.048   0.138    396
  Planarity :  0.005   0.059    475
  Dihedral  :  5.212  40.310    358
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.10 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 27.49 %
    Favored  : 67.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.46), residues: 317
  helix: -0.28 (0.67), residues: 63
  sheet: -0.57 (0.58), residues: 78
  loop : -0.39 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 538 
 TYR   0.004   0.001   TYR H 613 
 PHE   0.012   0.002   PHE H 608 
 TRP   0.010   0.002   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2653)
  covalent geometry    : angle       0.65106 ( 3576)
  hydrogen bonds       : bond        0.03239 (   79)
  hydrogen bonds       : angle       5.30136 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7253 (mmt180) cc_final: 0.7043 (mmp80)
REVERT: A   64 ARG cc_start: 0.7069 (mpt180) cc_final: 0.4492 (mpt180)
REVERT: H  575 LYS cc_start: 0.9185 (tttt) cc_final: 0.8487 (tptm)
REVERT: H  576 LEU cc_start: 0.8747 (mt) cc_final: 0.8496 (mt)
REVERT: H  587 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7268 (mt-10)
REVERT: H  590 PHE cc_start: 0.8007 (m-80) cc_final: 0.7728 (m-80)
REVERT: H  596 LEU cc_start: 0.9416 (tp) cc_final: 0.9193 (tp)
REVERT: H  597 GLN cc_start: 0.9398 (tp-100) cc_final: 0.9174 (tp-100)
REVERT: H  598 ILE cc_start: 0.9402 (mm) cc_final: 0.9193 (mp)
REVERT: H  600 PHE cc_start: 0.9408 (m-80) cc_final: 0.8846 (m-80)
REVERT: H  601 ASP cc_start: 0.9074 (m-30) cc_final: 0.8468 (m-30)
REVERT: H  614 LYS cc_start: 0.9371 (pttt) cc_final: 0.8921 (ptpp)
REVERT: H  626 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8767 (mm-40)
REVERT: H  628 ASP cc_start: 0.8903 (t0) cc_final: 0.8476 (t0)
REVERT: H  632 SER cc_start: 0.8913 (p) cc_final: 0.8670 (t)
REVERT: H  633 LEU cc_start: 0.9615 (mm) cc_final: 0.9269 (mm)
REVERT: H  642 GLU cc_start: 0.8185 (pp20) cc_final: 0.7137 (pm20)
REVERT: I  234 ARG cc_start: 0.8675 (mtm110) cc_final: 0.8388 (mtm110)
  outliers start: 14
  outliers final: 11
  residues processed: 81
  average time/residue: 0.0849
  time to fit residues: 7.9208
Evaluate side-chains
  83 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0270
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0030
   chunk 19 optimal weight:    9.9990
   chunk 4 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4048

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.143189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.096349 restraints weight = 4774.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 4.16
r_work: 0.3124 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2653  Z= 0.135
  Angle     :  0.668   8.509   3576  Z= 0.346
  Chirality :  0.047   0.134    396
  Planarity :  0.005   0.060    475
  Dihedral  :  5.083  39.821    358
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.42 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 29.55 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.46), residues: 317
  helix: -0.32 (0.66), residues: 63
  sheet: -0.56 (0.59), residues: 78
  loop : -0.24 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 588 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.008   0.001   PHE A  52 
 TRP   0.009   0.002   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2653)
  covalent geometry    : angle       0.66814 ( 3576)
  hydrogen bonds       : bond        0.03093 (   79)
  hydrogen bonds       : angle       5.22974 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ARG cc_start: 0.7065 (mpt180) cc_final: 0.4478 (mpt180)
REVERT: A  136 LYS cc_start: 0.8838 (tttt) cc_final: 0.8597 (mtpt)
REVERT: A  148 LYS cc_start: 0.9085 (tttp) cc_final: 0.8753 (ttpt)
REVERT: A  190 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8212 (mmmt)
REVERT: H  575 LYS cc_start: 0.9180 (tttt) cc_final: 0.8578 (tptm)
REVERT: H  576 LEU cc_start: 0.8694 (mt) cc_final: 0.8464 (mt)
REVERT: H  587 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7265 (mt-10)
REVERT: H  590 PHE cc_start: 0.8142 (m-80) cc_final: 0.7816 (m-80)
REVERT: H  596 LEU cc_start: 0.9545 (tp) cc_final: 0.9222 (tp)
REVERT: H  597 GLN cc_start: 0.9433 (tp-100) cc_final: 0.9119 (tp-100)
REVERT: H  598 ILE cc_start: 0.9436 (mm) cc_final: 0.9200 (mp)
REVERT: H  600 PHE cc_start: 0.9417 (m-80) cc_final: 0.8629 (m-80)
REVERT: H  601 ASP cc_start: 0.9079 (m-30) cc_final: 0.8435 (m-30)
REVERT: H  614 LYS cc_start: 0.9378 (pttt) cc_final: 0.8930 (ptpp)
REVERT: H  626 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8805 (mm-40)
REVERT: H  628 ASP cc_start: 0.8914 (t0) cc_final: 0.8474 (t0)
REVERT: H  632 SER cc_start: 0.8888 (p) cc_final: 0.8644 (t)
REVERT: H  633 LEU cc_start: 0.9623 (mm) cc_final: 0.9252 (mm)
REVERT: H  642 GLU cc_start: 0.8152 (pp20) cc_final: 0.7106 (pm20)
REVERT: I  234 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8383 (mtp-110)
REVERT: I  236 ASP cc_start: 0.8405 (p0) cc_final: 0.7609 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0972
  time to fit residues: 9.7334
Evaluate side-chains
  84 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** H 546 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 = 0.3996 r_free = 0.3996 target = 0.143313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.095465 restraints weight = 4791.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 4.27
r_work: 0.3070 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2653  Z= 0.157
  Angle     :  0.696   8.753   3576  Z= 0.359
  Chirality :  0.048   0.136    396
  Planarity :  0.005   0.059    475
  Dihedral  :  5.091  39.092    358
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.10 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 29.21 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.47), residues: 317
  helix: -0.19 (0.67), residues: 63
  sheet: -0.62 (0.59), residues: 78
  loop : -0.20 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  22 
 TYR   0.003   0.001   TYR A 138 
 PHE   0.010   0.002   PHE H 608 
 TRP   0.009   0.002   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 2653)
  covalent geometry    : angle       0.69570 ( 3576)
  hydrogen bonds       : bond        0.03164 (   79)
  hydrogen bonds       : angle       5.23471 (  228)

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

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

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  634 Ramachandran restraints generated.
    317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ARG cc_start: 0.7071 (mpt180) cc_final: 0.4465 (mpt180)
REVERT: H  575 LYS cc_start: 0.9189 (tttt) cc_final: 0.8582 (tptm)
REVERT: H  576 LEU cc_start: 0.8769 (mt) cc_final: 0.8486 (mt)
REVERT: H  587 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7327 (mt-10)
REVERT: H  590 PHE cc_start: 0.8199 (m-80) cc_final: 0.7823 (m-80)
REVERT: H  596 LEU cc_start: 0.9374 (tp) cc_final: 0.9079 (tp)
REVERT: H  597 GLN cc_start: 0.9394 (tp-100) cc_final: 0.9106 (tp-100)
REVERT: H  600 PHE cc_start: 0.9421 (m-80) cc_final: 0.8613 (m-80)
REVERT: H  601 ASP cc_start: 0.9052 (m-30) cc_final: 0.8406 (m-30)
REVERT: H  614 LYS cc_start: 0.9343 (pttt) cc_final: 0.8873 (ptpp)
REVERT: H  626 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8809 (mm-40)
REVERT: H  628 ASP cc_start: 0.8923 (t0) cc_final: 0.8487 (t0)
REVERT: H  632 SER cc_start: 0.8822 (p) cc_final: 0.8574 (t)
REVERT: H  633 LEU cc_start: 0.9636 (mm) cc_final: 0.9346 (mm)
REVERT: H  642 GLU cc_start: 0.8154 (pp20) cc_final: 0.7562 (pm20)
REVERT: I  234 ARG cc_start: 0.8647 (mtm110) cc_final: 0.8324 (mtm110)
  outliers start: 13
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0785
  time to fit residues: 7.6883
Evaluate side-chains
  88 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain H residue  533 MET
Chi-restraints excluded: chain H residue  539 LEU
Chi-restraints excluded: chain H residue  551 GLU
Chi-restraints excluded: chain H residue  557 LEU
Chi-restraints excluded: chain H residue  624 VAL
Chi-restraints excluded: chain H residue  643 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0040
   chunk 22 optimal weight:    6.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.142869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095991 restraints weight = 4728.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 4.18
r_work: 0.3134 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2653  Z= 0.149
  Angle     :  0.693   8.693   3576  Z= 0.357
  Chirality :  0.048   0.135    396
  Planarity :  0.005   0.059    475
  Dihedral  :  5.041  38.654    358
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.42 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 29.55 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.47), residues: 317
  helix: -0.19 (0.67), residues: 63
  sheet: -0.68 (0.59), residues: 78
  loop : -0.20 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 588 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.012   0.002   PHE H 600 
 TRP   0.008   0.002   TRP H 610 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2653)
  covalent geometry    : angle       0.69283 ( 3576)
  hydrogen bonds       : bond        0.03071 (   79)
  hydrogen bonds       : angle       5.20254 (  228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1036.31 seconds
wall clock time: 18 minutes 25.75 seconds (1105.75 seconds total)