Starting phenix.real_space_refine
on Thu Jun  5 21:09:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f25_50138/06_2025/9f25_50138.cif"
  }
  resolution = 3.7
  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=   0.034
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      19      5.16       5
     C    4331      2.51       5
     N    1079      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6717
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 830, 6717
          Classifications: {'peptide': 830}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 28, 'TRANS': 801}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 4.75, per 1000 atoms: 0.71
  Number of scatterers: 6717
  At special positions: 0
  Unit cell: (105.95, 70.85, 109.85, 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      19     16.00
     O    1288      8.00
     N    1079      7.00
     C    4331      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 454 " distance=2.00

  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: 1.71
  Conformation dependent library (CDL) restraints added in 950.6 milliseconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      46.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 80 through 101
      removed outlier: 3.716A  pdb=" N   THR A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
    Processing helix  chain 'A' and resid 130 through 132
      No H-bonds generated for 'chain 'A' and resid 130 through 132'
    Processing helix  chain 'A' and resid 216 through 233
      removed outlier: 3.631A  pdb=" N   THR A 220 " --> pdb=" O   ASP A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
    Processing helix  chain 'A' and resid 268 through 274
      removed outlier: 3.543A  pdb=" N   PHE A 273 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE A 274 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 300
    Processing helix  chain 'A' and resid 309 through 322
      removed outlier: 3.570A  pdb=" N   MET A 313 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 347
    Processing helix  chain 'A' and resid 350 through 359
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 3.555A  pdb=" N   PHE A 413 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 496 through 505
    Processing helix  chain 'A' and resid 549 through 556
    Processing helix  chain 'A' and resid 571 through 578
    Processing helix  chain 'A' and resid 587 through 596
      removed outlier: 3.535A  pdb=" N   VAL A 591 " --> pdb=" O   SER A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 619
      removed outlier: 4.085A  pdb=" N   GLU A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 641
    Processing helix  chain 'A' and resid 648 through 660
    Processing helix  chain 'A' and resid 661 through 663
      No H-bonds generated for 'chain 'A' and resid 661 through 663'
    Processing helix  chain 'A' and resid 687 through 721
    Processing helix  chain 'A' and resid 721 through 753
    Processing helix  chain 'A' and resid 755 through 763
    Processing helix  chain 'A' and resid 765 through 800
      removed outlier: 3.661A  pdb=" N   LEU A 769 " --> pdb=" O   ASN A 765 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASN A 783 " --> pdb=" O   LYS A 779 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 796 " --> pdb=" O   SER A 792 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 824
      removed outlier: 3.557A  pdb=" N   GLY A 804 " --> pdb=" O   MET A 800 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP A 817 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA A 818 " --> pdb=" O   SER A 814 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR A 824 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 846
    Processing helix  chain 'A' and resid 852 through 856
      removed outlier: 3.606A  pdb=" N   LYS A 855 " --> pdb=" O   GLN A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 868
      removed outlier: 4.217A  pdb=" N   GLU A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148
      removed outlier: 4.225A  pdb=" N   TYR A  21 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   LYS A  34 " --> pdb=" O   PRO A  46 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE A  42 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 155 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   GLU A  47 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL A 152 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214
    Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 325
    Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 458
      removed outlier: 9.270A  pdb=" N   TYR A 543 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A 428 " --> pdb=" O   TYR A 543 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481
    Processing sheet with id=AA7, first strand: chain 'A' and resid 567 through 569
      removed outlier: 6.411A  pdb=" N   ALA A 567 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    301 hydrogen bonds defined for protein.
    873 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: 2.01

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2141
        1.35 -     1.47: 1669
        1.47 -     1.59: 3019
        1.59 -     1.71: 0
        1.71 -     1.83: 33
  Bond restraints: 6862
  Sorted by residual:
  bond pdb=" C   ALA A 601 "
       pdb=" N   MET A 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.376 -0.044 1.29e-02 6.01e+03 1.16e+01
  bond pdb=" C   VAL A 611 "
       pdb=" N   TYR A 612 "
    ideal  model  delta    sigma   weight residual
    1.335  1.371 -0.036 1.36e-02 5.41e+03 7.15e+00
  bond pdb=" C   LYS A 456 "
       pdb=" N   VAL A 457 "
    ideal  model  delta    sigma   weight residual
    1.331  1.309  0.021 1.27e-02 6.20e+03 2.86e+00
  bond pdb=" CB  GLU A 708 "
       pdb=" CG  GLU A 708 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CB  GLU A 535 "
       pdb=" CG  GLU A 535 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.64e-01
  ... (remaining 6857 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 9183
        2.00 -     4.00: 91
        4.00 -     5.99: 18
        5.99 -     7.99: 1
        7.99 -     9.99: 1
  Bond angle restraints: 9294
  Sorted by residual:
  angle pdb=" CB  MET A 646 "
        pdb=" CG  MET A 646 "
        pdb=" SD  MET A 646 "
      ideal   model   delta    sigma   weight residual
     112.70  102.71    9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CA  GLU A 708 "
        pdb=" CB  GLU A 708 "
        pdb=" CG  GLU A 708 "
      ideal   model   delta    sigma   weight residual
     114.10  119.23   -5.13 2.00e+00 2.50e-01 6.58e+00
  angle pdb=" CB  GLU A 708 "
        pdb=" CG  GLU A 708 "
        pdb=" CD  GLU A 708 "
      ideal   model   delta    sigma   weight residual
     112.60  116.93   -4.33 1.70e+00 3.46e-01 6.50e+00
  angle pdb=" CA  MET A 646 "
        pdb=" CB  MET A 646 "
        pdb=" CG  MET A 646 "
      ideal   model   delta    sigma   weight residual
     114.10  119.06   -4.96 2.00e+00 2.50e-01 6.16e+00
  angle pdb=" CA  GLN A 753 "
        pdb=" CB  GLN A 753 "
        pdb=" CG  GLN A 753 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.89e+00
  ... (remaining 9289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3531
       17.77 -    35.53: 444
       35.53 -    53.29: 107
       53.29 -    71.06: 20
       71.06 -    88.82: 9
  Dihedral angle restraints: 4111
    sinusoidal: 1656
      harmonic: 2455
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 454 "
           pdb=" CB  CYS A 454 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.47   34.53     1      1.00e+01 1.00e-02 1.69e+01
  dihedral pdb=" CA  MET A 646 "
           pdb=" C   MET A 646 "
           pdb=" N   LEU A 647 "
           pdb=" CA  LEU A 647 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ALA A  20 "
           pdb=" C   ALA A  20 "
           pdb=" N   TYR A  21 "
           pdb=" CA  TYR A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 680
       0.031 -    0.062: 230
       0.062 -    0.093: 77
       0.093 -    0.124: 41
       0.124 -    0.155: 8
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" CB  ILE A 633 "
            pdb=" CA  ILE A 633 "
            pdb=" CG1 ILE A 633 "
            pdb=" CG2 ILE A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  ILE A 154 "
            pdb=" N   ILE A 154 "
            pdb=" C   ILE A 154 "
            pdb=" CB  ILE A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  ILE A  19 "
            pdb=" N   ILE A  19 "
            pdb=" C   ILE A  19 "
            pdb=" CB  ILE A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1033 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 634 "   -0.038 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO A 635 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 635 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 635 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 753 "    0.009 2.00e-02 2.50e+03   1.79e-02 3.19e+00
        pdb=" C   GLN A 753 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLN A 753 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 754 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  24 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A  25 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A  25 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  25 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 540
        2.74 -     3.28: 6962
        3.28 -     3.82: 11164
        3.82 -     4.36: 12487
        4.36 -     4.90: 22017
  Nonbonded interactions: 53170
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 121 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OH  TYR A 583 "
            pdb=" O   PRO A 639 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   GLY A 179 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NE2 HIS A 230 "
            pdb=" O   LEU A 345 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASP A 726 "
            pdb=" NH2 ARG A 729 "
     model   vdw
     2.278 3.120
  ... (remaining 53165 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.700
  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:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.630
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
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      :  0.002   0.044   6863  Z= 0.120
  Angle     :  0.533   9.988   9296  Z= 0.279
  Chirality :  0.040   0.155   1036
  Planarity :  0.004   0.059   1194
  Dihedral  : 16.769  88.824   2524
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 22.89 %
    Favored  : 76.97 %
  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:  0.58 (0.30), residues: 822
  helix:  1.97 (0.28), residues: 370
  sheet: -0.58 (0.55), residues: 79
  loop : -1.07 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.013   0.001   PHE A 366 
 TYR   0.013   0.001   TYR A 636 
 ARG   0.003   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13764 (  301)
  hydrogen bonds       : angle       5.03809 (  873)
  SS BOND              : bond        0.03197 (    1)
  SS BOND              : angle       5.13780 (    2)
  covalent geometry    : bond        0.00238 ( 6862)
  covalent geometry    : angle       0.52756 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1643
  time to fit residues: 21.1884
Evaluate side-chains
  81 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  67 GLN
A 133 ASN
A 470 ASN
A 533 ASN
A 539 ASN
A 642 ASN
A 693 GLN
A 763 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.158027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133652 restraints weight = 10803.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137530 restraints weight = 6654.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.140249 restraints weight = 4764.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6863  Z= 0.129
  Angle     :  0.510   7.480   9296  Z= 0.268
  Chirality :  0.041   0.162   1036
  Planarity :  0.003   0.037   1194
  Dihedral  :  3.799  18.339    891
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.02 %
    Favored  : 76.31 %
  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:  0.87 (0.30), residues: 822
  helix:  2.25 (0.28), residues: 365
  sheet: -0.53 (0.59), residues: 67
  loop : -0.89 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.009   0.001   PHE A  36 
 TYR   0.013   0.001   TYR A 636 
 ARG   0.004   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  301)
  hydrogen bonds       : angle       4.13084 (  873)
  SS BOND              : bond        0.00675 (    1)
  SS BOND              : angle       1.63615 (    2)
  covalent geometry    : bond        0.00298 ( 6862)
  covalent geometry    : angle       0.50935 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7644 (mmtt)
REVERT: A  312 TYR cc_start: 0.8488 (t80) cc_final: 0.8190 (t80)
REVERT: A  697 ASN cc_start: 0.6716 (m-40) cc_final: 0.6332 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1642
  time to fit residues: 24.0324
Evaluate side-chains
  95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  863 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0470
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 693 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.162808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138583 restraints weight = 10648.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.142631 restraints weight = 6355.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145395 restraints weight = 4493.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6863  Z= 0.110
  Angle     :  0.508  10.936   9296  Z= 0.261
  Chirality :  0.041   0.167   1036
  Planarity :  0.003   0.035   1194
  Dihedral  :  3.748  19.804    891
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.88 %
    Favored  : 76.31 %
  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:  0.91 (0.30), residues: 822
  helix:  2.32 (0.28), residues: 366
  sheet: -0.52 (0.59), residues: 67
  loop : -0.91 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.009   0.001   PHE A  36 
 TYR   0.011   0.001   TYR A 636 
 ARG   0.004   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  301)
  hydrogen bonds       : angle       3.95079 (  873)
  SS BOND              : bond        0.00859 (    1)
  SS BOND              : angle       1.38839 (    2)
  covalent geometry    : bond        0.00249 ( 6862)
  covalent geometry    : angle       0.50758 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8500 (t80) cc_final: 0.8220 (t80)
REVERT: A  697 ASN cc_start: 0.6647 (m-40) cc_final: 0.6312 (t0)
REVERT: A  801 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6475 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1455
  time to fit residues: 22.4341
Evaluate side-chains
  98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 224 GLN
A 642 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132369 restraints weight = 10807.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136314 restraints weight = 6695.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.138989 restraints weight = 4838.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6863  Z= 0.182
  Angle     :  0.561   8.107   9296  Z= 0.288
  Chirality :  0.043   0.174   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.943  21.824    891
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 19.95 %
    Favored  : 74.97 %
  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:  0.64 (0.29), residues: 822
  helix:  2.07 (0.28), residues: 366
  sheet: -0.72 (0.58), residues: 67
  loop : -1.01 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 606 
 HIS   0.005   0.002   HIS A 223 
 PHE   0.010   0.001   PHE A 585 
 TYR   0.015   0.002   TYR A 384 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  301)
  hydrogen bonds       : angle       4.01242 (  873)
  SS BOND              : bond        0.00863 (    1)
  SS BOND              : angle       1.86242 (    2)
  covalent geometry    : bond        0.00429 ( 6862)
  covalent geometry    : angle       0.56040 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 86
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8387 (m-40) cc_final: 0.8145 (m110)
REVERT: A  312 TYR cc_start: 0.8565 (t80) cc_final: 0.8334 (t80)
REVERT: A  400 ASN cc_start: 0.8415 (m-40) cc_final: 0.8041 (t0)
REVERT: A  456 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7584 (mtpp)
REVERT: A  681 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7765 (mt)
REVERT: A  697 ASN cc_start: 0.6637 (m-40) cc_final: 0.6384 (t0)
REVERT: A  801 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6559 (mm)
  outliers start: 38
  outliers final: 25
  residues processed: 112
  average time/residue: 0.1592
  time to fit residues: 25.5361
Evaluate side-chains
  114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  863 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   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 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.157236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132730 restraints weight = 10660.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.136726 restraints weight = 6466.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139380 restraints weight = 4580.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6863  Z= 0.120
  Angle     :  0.514   7.685   9296  Z= 0.264
  Chirality :  0.041   0.181   1036
  Planarity :  0.003   0.039   1194
  Dihedral  :  3.846  21.897    891
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 21.15 %
    Favored  : 75.10 %
  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:  0.71 (0.30), residues: 822
  helix:  2.18 (0.28), residues: 366
  sheet: -0.69 (0.58), residues: 67
  loop : -1.02 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.008   0.001   PHE A 338 
 TYR   0.011   0.001   TYR A 384 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  301)
  hydrogen bonds       : angle       3.90193 (  873)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       1.88769 (    2)
  covalent geometry    : bond        0.00278 ( 6862)
  covalent geometry    : angle       0.51338 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8439 (m-40) cc_final: 0.8193 (m110)
REVERT: A  312 TYR cc_start: 0.8540 (t80) cc_final: 0.8297 (t80)
REVERT: A  400 ASN cc_start: 0.8373 (m-40) cc_final: 0.8042 (t0)
REVERT: A  456 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7604 (mtpp)
REVERT: A  697 ASN cc_start: 0.6668 (m-40) cc_final: 0.6379 (t0)
REVERT: A  801 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6494 (mm)
  outliers start: 28
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1506
  time to fit residues: 23.8093
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.156536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132403 restraints weight = 10578.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.136423 restraints weight = 6331.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.139079 restraints weight = 4439.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6863  Z= 0.105
  Angle     :  0.502   7.099   9296  Z= 0.257
  Chirality :  0.041   0.167   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.742  21.589    891
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 20.75 %
    Favored  : 74.97 %
  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:  0.85 (0.30), residues: 822
  helix:  2.43 (0.28), residues: 360
  sheet: -0.65 (0.56), residues: 72
  loop : -1.04 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.008   0.001   PHE A  36 
 TYR   0.010   0.001   TYR A 384 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  301)
  hydrogen bonds       : angle       3.84390 (  873)
  SS BOND              : bond        0.00745 (    1)
  SS BOND              : angle       1.47287 (    2)
  covalent geometry    : bond        0.00237 ( 6862)
  covalent geometry    : angle       0.50196 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8437 (m-40) cc_final: 0.8181 (m110)
REVERT: A  312 TYR cc_start: 0.8524 (t80) cc_final: 0.8288 (t80)
REVERT: A  400 ASN cc_start: 0.8332 (m-40) cc_final: 0.8017 (t0)
REVERT: A  456 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7610 (mtpp)
REVERT: A  697 ASN cc_start: 0.6626 (m-40) cc_final: 0.6341 (t0)
REVERT: A  801 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6384 (mm)
  outliers start: 32
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1589
  time to fit residues: 26.9509
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 75 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** 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 = 0.4017 r_free = 0.4017 target = 0.161166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.136791 restraints weight = 10586.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140785 restraints weight = 6481.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143453 restraints weight = 4610.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6863  Z= 0.111
  Angle     :  0.542  13.342   9296  Z= 0.269
  Chirality :  0.041   0.165   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.740  21.852    891
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.69 %
    Favored  : 74.70 %
  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:  0.87 (0.30), residues: 822
  helix:  2.41 (0.28), residues: 360
  sheet: -0.49 (0.58), residues: 72
  loop : -1.02 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.013   0.001   PHE A 413 
 TYR   0.010   0.001   TYR A 384 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  301)
  hydrogen bonds       : angle       3.84907 (  873)
  SS BOND              : bond        0.00627 (    1)
  SS BOND              : angle       1.61423 (    2)
  covalent geometry    : bond        0.00254 ( 6862)
  covalent geometry    : angle       0.54118 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8399 (m-40) cc_final: 0.8139 (m110)
REVERT: A  312 TYR cc_start: 0.8516 (t80) cc_final: 0.8241 (t80)
REVERT: A  400 ASN cc_start: 0.8295 (m-40) cc_final: 0.8038 (t0)
REVERT: A  456 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7622 (mtpp)
REVERT: A  697 ASN cc_start: 0.6625 (m-40) cc_final: 0.6341 (t0)
REVERT: A  801 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6485 (mm)
  outliers start: 27
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1460
  time to fit residues: 23.6457
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  687 ASN
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 76 optimal weight:    0.0170
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0470
   chunk 15 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.158677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.133178 restraints weight = 10658.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.137358 restraints weight = 6373.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140211 restraints weight = 4480.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6863  Z= 0.104
  Angle     :  0.526  12.134   9296  Z= 0.263
  Chirality :  0.041   0.175   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.706  21.341    891
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.55 %
    Favored  : 75.10 %
  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:  0.92 (0.30), residues: 822
  helix:  2.44 (0.28), residues: 360
  sheet: -0.45 (0.58), residues: 72
  loop : -0.98 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.010   0.001   PHE A 413 
 TYR   0.009   0.001   TYR A 384 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  301)
  hydrogen bonds       : angle       3.82168 (  873)
  SS BOND              : bond        0.00778 (    1)
  SS BOND              : angle       1.47550 (    2)
  covalent geometry    : bond        0.00239 ( 6862)
  covalent geometry    : angle       0.52559 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8405 (m-40) cc_final: 0.8161 (m110)
REVERT: A  312 TYR cc_start: 0.8526 (t80) cc_final: 0.8254 (t80)
REVERT: A  400 ASN cc_start: 0.8285 (m-40) cc_final: 0.8017 (t0)
REVERT: A  456 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7637 (mtpp)
REVERT: A  697 ASN cc_start: 0.6635 (m-40) cc_final: 0.6345 (t0)
REVERT: A  801 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6494 (mm)
  outliers start: 25
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1443
  time to fit residues: 23.2210
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.155420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.131014 restraints weight = 10656.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.134919 restraints weight = 6431.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.137588 restraints weight = 4546.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6863  Z= 0.135
  Angle     :  0.558  11.152   9296  Z= 0.276
  Chirality :  0.041   0.178   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.804  22.071    891
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.42 %
    Favored  : 75.10 %
  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:  0.79 (0.30), residues: 822
  helix:  2.31 (0.28), residues: 360
  sheet: -0.55 (0.58), residues: 72
  loop : -1.02 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 706 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.014   0.001   PHE A 192 
 TYR   0.016   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  301)
  hydrogen bonds       : angle       3.86161 (  873)
  SS BOND              : bond        0.00689 (    1)
  SS BOND              : angle       1.67838 (    2)
  covalent geometry    : bond        0.00321 ( 6862)
  covalent geometry    : angle       0.55706 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.8062 (mttp) cc_final: 0.7831 (mttm)
REVERT: A  248 ASN cc_start: 0.8461 (m-40) cc_final: 0.8200 (m110)
REVERT: A  312 TYR cc_start: 0.8573 (t80) cc_final: 0.8297 (t80)
REVERT: A  400 ASN cc_start: 0.8307 (m-40) cc_final: 0.8012 (t0)
REVERT: A  456 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7649 (mtpp)
REVERT: A  697 ASN cc_start: 0.6663 (m-40) cc_final: 0.6422 (t0)
REVERT: A  732 MET cc_start: 0.8240 (tpt) cc_final: 0.7937 (tpt)
REVERT: A  801 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6400 (mm)
  outliers start: 26
  outliers final: 20
  residues processed: 107
  average time/residue: 0.1460
  time to fit residues: 22.8259
Evaluate side-chains
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.155620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.129888 restraints weight = 10854.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133992 restraints weight = 6525.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136820 restraints weight = 4608.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6863  Z= 0.156
  Angle     :  0.578  10.511   9296  Z= 0.287
  Chirality :  0.042   0.179   1036
  Planarity :  0.003   0.039   1194
  Dihedral  :  3.922  22.611    891
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.29 %
    Favored  : 75.37 %
  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:  0.68 (0.30), residues: 822
  helix:  2.18 (0.28), residues: 360
  sheet: -0.59 (0.58), residues: 72
  loop : -1.04 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 706 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.013   0.001   PHE A 192 
 TYR   0.015   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  301)
  hydrogen bonds       : angle       3.91767 (  873)
  SS BOND              : bond        0.00855 (    1)
  SS BOND              : angle       1.92028 (    2)
  covalent geometry    : bond        0.00374 ( 6862)
  covalent geometry    : angle       0.57749 ( 9294)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8398 (m-40) cc_final: 0.8122 (m110)
REVERT: A  312 TYR cc_start: 0.8580 (t80) cc_final: 0.8309 (t80)
REVERT: A  400 ASN cc_start: 0.8320 (m-40) cc_final: 0.8104 (t0)
REVERT: A  456 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (mtpp)
REVERT: A  697 ASN cc_start: 0.6629 (m-40) cc_final: 0.6426 (t0)
REVERT: A  732 MET cc_start: 0.8314 (tpt) cc_final: 0.8017 (tpt)
REVERT: A  801 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6607 (mm)
REVERT: A  812 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7598 (t0)
  outliers start: 25
  outliers final: 22
  residues processed: 107
  average time/residue: 0.1508
  time to fit residues: 23.4547
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0870
   chunk 81 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.157993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.133496 restraints weight = 10567.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.137505 restraints weight = 6373.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.140258 restraints weight = 4509.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6863  Z= 0.105
  Angle     :  0.555  10.074   9296  Z= 0.271
  Chirality :  0.040   0.177   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.818  21.463    891
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.95 %
    Favored  : 75.10 %
  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:  0.80 (0.30), residues: 822
  helix:  2.31 (0.28), residues: 360
  sheet: -0.60 (0.58), residues: 72
  loop : -1.01 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.017   0.001   PHE A 366 
 TYR   0.014   0.001   TYR A 856 
 ARG   0.011   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  301)
  hydrogen bonds       : angle       3.82499 (  873)
  SS BOND              : bond        0.00646 (    1)
  SS BOND              : angle       1.55758 (    2)
  covalent geometry    : bond        0.00241 ( 6862)
  covalent geometry    : angle       0.55435 ( 9294)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2511.72 seconds
wall clock time: 44 minutes 17.54 seconds (2657.54 seconds total)