Starting phenix.real_space_refine
on Sat May 10 18:39:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f25_50138/05_2025/9f25_50138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f25_50138/05_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_50138/05_2025/9f25_50138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f25_50138/05_2025/9f25_50138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f25_50138/05_2025/9f25_50138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f25_50138/05_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-5687/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: 4.82, per 1000 atoms: 0.72
  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: 1.66
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.74
  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: 1.90

  Time building geometry restraints manager: 1.93 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:             1.710
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.580
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.750
-------------------------------------------------------------------------------
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  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1664
  time to fit residues: 21.5302
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  : 0.704 
-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.155778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131749 restraints weight = 10662.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.135766 restraints weight = 6452.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.138488 restraints weight = 4572.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.0967

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   7.461   9296  Z= 0.268
  Chirality :  0.041   0.161   1036
  Planarity :  0.003   0.037   1194
  Dihedral  :  3.799  18.301    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  : 20.88 %
    Favored  : 76.44 %
  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:  2.26 (0.28), residues: 365
  sheet: -0.53 (0.59), residues: 67
  loop : -0.88 (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        0.03946 (  301)
  hydrogen bonds       : angle       4.13519 (  873)
  SS BOND              : bond        0.00573 (    1)
  SS BOND              : angle       1.65468 (    2)
  covalent geometry    : bond        0.00298 ( 6862)
  covalent geometry    : angle       0.50921 ( 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  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7634 (mmtt)
REVERT: A  312 TYR cc_start: 0.8477 (t80) cc_final: 0.8180 (t80)
REVERT: A  697 ASN cc_start: 0.6684 (m-40) cc_final: 0.6314 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1660
  time to fit residues: 24.3718
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  : 0.738 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.163297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139053 restraints weight = 10648.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.143106 restraints weight = 6371.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.145876 restraints weight = 4489.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6863  Z= 0.107
  Angle     :  0.508  11.005   9296  Z= 0.260
  Chirality :  0.040   0.169   1036
  Planarity :  0.003   0.036   1194
  Dihedral  :  3.747  20.256    891
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.29 %
    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:  0.93 (0.30), residues: 822
  helix:  2.34 (0.28), residues: 366
  sheet: -0.52 (0.59), residues: 67
  loop : -0.90 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.009   0.001   PHE A  36 
 TYR   0.013   0.001   TYR A 321 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  301)
  hydrogen bonds       : angle       3.94652 (  873)
  SS BOND              : bond        0.00764 (    1)
  SS BOND              : angle       1.44225 (    2)
  covalent geometry    : bond        0.00238 ( 6862)
  covalent geometry    : angle       0.50733 ( 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
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8481 (t80) cc_final: 0.8186 (t80)
REVERT: A  697 ASN cc_start: 0.6645 (m-40) cc_final: 0.6312 (t0)
REVERT: A  801 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6456 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1437
  time to fit residues: 21.9156
Evaluate side-chains
  96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  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  431 VAL
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  784 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.157636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132958 restraints weight = 10811.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.136818 restraints weight = 6610.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139494 restraints weight = 4741.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6863  Z= 0.203
  Angle     :  0.582   8.267   9296  Z= 0.299
  Chirality :  0.044   0.176   1036
  Planarity :  0.003   0.039   1194
  Dihedral  :  4.016  22.059    891
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 19.81 %
    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:  0.58 (0.29), residues: 822
  helix:  2.01 (0.28), residues: 366
  sheet: -0.71 (0.59), residues: 67
  loop : -1.05 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 606 
 HIS   0.005   0.002   HIS A 223 
 PHE   0.011   0.002   PHE A 851 
 TYR   0.016   0.002   TYR A 384 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  301)
  hydrogen bonds       : angle       4.07216 (  873)
  SS BOND              : bond        0.00935 (    1)
  SS BOND              : angle       1.77151 (    2)
  covalent geometry    : bond        0.00483 ( 6862)
  covalent geometry    : angle       0.58110 ( 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  : 0.707 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8457 (m-40) cc_final: 0.8217 (m110)
REVERT: A  312 TYR cc_start: 0.8585 (t80) cc_final: 0.8352 (t80)
REVERT: A  400 ASN cc_start: 0.8438 (m-40) cc_final: 0.8050 (t0)
REVERT: A  456 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7595 (mtpp)
REVERT: A  681 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7799 (mt)
REVERT: A  697 ASN cc_start: 0.6666 (m-40) cc_final: 0.6406 (t0)
REVERT: A  774 ASN cc_start: 0.7256 (m-40) cc_final: 0.6990 (t0)
REVERT: A  801 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6634 (mm)
  outliers start: 38
  outliers final: 26
  residues processed: 112
  average time/residue: 0.1541
  time to fit residues: 24.7689
Evaluate side-chains
  115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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  422 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  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:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.157322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132666 restraints weight = 10648.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136701 restraints weight = 6469.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139300 restraints weight = 4585.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.1623

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= 0.119
  Angle     :  0.520   8.760   9296  Z= 0.267
  Chirality :  0.041   0.168   1036
  Planarity :  0.003   0.039   1194
  Dihedral  :  3.905  22.851    891
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.21 %
    Favored  : 75.64 %
  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:  0.73 (0.30), residues: 822
  helix:  2.17 (0.28), residues: 366
  sheet: -0.64 (0.59), residues: 67
  loop : -0.99 (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   0.012   0.001   TYR A 384 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  301)
  hydrogen bonds       : angle       3.93254 (  873)
  SS BOND              : bond        0.00904 (    1)
  SS BOND              : angle       1.88051 (    2)
  covalent geometry    : bond        0.00272 ( 6862)
  covalent geometry    : angle       0.51961 ( 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
  122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8456 (m-40) cc_final: 0.8200 (m110)
REVERT: A  312 TYR cc_start: 0.8559 (t80) cc_final: 0.8315 (t80)
REVERT: A  400 ASN cc_start: 0.8386 (m-40) cc_final: 0.8043 (t0)
REVERT: A  456 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7599 (mtpp)
REVERT: A  697 ASN cc_start: 0.6702 (m-40) cc_final: 0.6397 (t0)
REVERT: A  801 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6481 (mm)
  outliers start: 31
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1581
  time to fit residues: 25.5172
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   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 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130076 restraints weight = 10670.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133986 restraints weight = 6523.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.136642 restraints weight = 4672.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6863  Z= 0.127
  Angle     :  0.526   8.996   9296  Z= 0.268
  Chirality :  0.041   0.168   1036
  Planarity :  0.003   0.039   1194
  Dihedral  :  3.865  21.869    891
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.75 %
    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:  0.81 (0.30), residues: 822
  helix:  2.29 (0.28), residues: 360
  sheet: -0.56 (0.61), residues: 67
  loop : -0.97 (0.30), residues: 395

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   0.008   0.001   PHE A 338 
 TYR   0.011   0.001   TYR A 384 
 ARG   0.003   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  301)
  hydrogen bonds       : angle       3.90087 (  873)
  SS BOND              : bond        0.00737 (    1)
  SS BOND              : angle       1.56987 (    2)
  covalent geometry    : bond        0.00296 ( 6862)
  covalent geometry    : angle       0.52593 ( 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
  123 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8427 (m-40) cc_final: 0.8161 (m110)
REVERT: A  312 TYR cc_start: 0.8567 (t80) cc_final: 0.8319 (t80)
REVERT: A  400 ASN cc_start: 0.8341 (m-40) cc_final: 0.8053 (t0)
REVERT: A  456 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7619 (mtpp)
REVERT: A  697 ASN cc_start: 0.6648 (m-40) cc_final: 0.6397 (t0)
REVERT: A  801 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6450 (mm)
  outliers start: 29
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1624
  time to fit residues: 26.4362
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  : 0.841 
-------------------------------------------------------------------------------
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  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  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:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0570
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.4556

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.162729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138523 restraints weight = 10583.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142544 restraints weight = 6464.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145273 restraints weight = 4590.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6863  Z= 0.101
  Angle     :  0.532  13.100   9296  Z= 0.265
  Chirality :  0.041   0.176   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.769  20.354    891
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.02 %
    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:  0.93 (0.30), residues: 822
  helix:  2.44 (0.28), residues: 360
  sheet: -0.35 (0.56), residues: 79
  loop : -1.00 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.009   0.001   PHE A  36 
 TYR   0.008   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  301)
  hydrogen bonds       : angle       3.88404 (  873)
  SS BOND              : bond        0.01145 (    1)
  SS BOND              : angle       1.49760 (    2)
  covalent geometry    : bond        0.00224 ( 6862)
  covalent geometry    : angle       0.53184 ( 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
  123 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8369 (m-40) cc_final: 0.8115 (m110)
REVERT: A  312 TYR cc_start: 0.8514 (t80) cc_final: 0.8237 (t80)
REVERT: A  400 ASN cc_start: 0.8253 (m-40) cc_final: 0.8034 (t0)
REVERT: A  456 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7618 (mtpp)
REVERT: A  697 ASN cc_start: 0.6655 (m-40) cc_final: 0.6355 (t0)
REVERT: A  801 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6495 (mm)
  outliers start: 27
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1564
  time to fit residues: 25.8659
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.158918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135015 restraints weight = 10676.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.138964 restraints weight = 6490.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141630 restraints weight = 4596.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1969

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     :  0.559  11.928   9296  Z= 0.278
  Chirality :  0.043   0.223   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.822  20.602    891
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.29 %
    Favored  : 75.23 %
  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:  0.83 (0.30), residues: 822
  helix:  2.34 (0.28), residues: 360
  sheet: -0.39 (0.56), residues: 79
  loop : -1.04 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.013   0.001   PHE A 413 
 TYR   0.015   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  301)
  hydrogen bonds       : angle       3.92203 (  873)
  SS BOND              : bond        0.00732 (    1)
  SS BOND              : angle       1.68381 (    2)
  covalent geometry    : bond        0.00317 ( 6862)
  covalent geometry    : angle       0.55897 ( 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
  113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.7984 (mttp) cc_final: 0.7744 (mttm)
REVERT: A  248 ASN cc_start: 0.8414 (m-40) cc_final: 0.8159 (m110)
REVERT: A  312 TYR cc_start: 0.8550 (t80) cc_final: 0.8276 (t80)
REVERT: A  400 ASN cc_start: 0.8276 (m-40) cc_final: 0.8053 (t0)
REVERT: A  456 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7647 (mtpp)
REVERT: A  697 ASN cc_start: 0.6634 (m-40) cc_final: 0.6404 (t0)
REVERT: A  801 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6545 (mm)
  outliers start: 26
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1446
  time to fit residues: 22.9310
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
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  350 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  430 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0050
   chunk 53 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.158040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.134624 restraints weight = 10575.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.138582 restraints weight = 6355.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.141243 restraints weight = 4491.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2007

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= 0.112
  Angle     :  0.551  11.217   9296  Z= 0.273
  Chirality :  0.042   0.224   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.791  20.303    891
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.95 %
    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:  2.38 (0.28), residues: 360
  sheet: -0.49 (0.58), residues: 72
  loop : -1.00 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.011   0.001   PHE A 354 
 TYR   0.013   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  301)
  hydrogen bonds       : angle       3.88208 (  873)
  SS BOND              : bond        0.00691 (    1)
  SS BOND              : angle       1.60457 (    2)
  covalent geometry    : bond        0.00259 ( 6862)
  covalent geometry    : angle       0.55099 ( 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
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8366 (m-40) cc_final: 0.8117 (m110)
REVERT: A  312 TYR cc_start: 0.8514 (t80) cc_final: 0.8247 (t80)
REVERT: A  456 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7653 (mtpp)
REVERT: A  646 MET cc_start: 0.4375 (ttt) cc_final: 0.4109 (ttt)
REVERT: A  801 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6465 (mm)
  outliers start: 25
  outliers final: 22
  residues processed: 111
  average time/residue: 0.1395
  time to fit residues: 22.6855
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  350 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  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  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 29 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    0.4980
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 ** 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 = 0.3922 r_free = 0.3922 target = 0.153296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127884 restraints weight = 10969.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.131856 restraints weight = 6611.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134595 restraints weight = 4699.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6863  Z= 0.200
  Angle     :  0.611  10.443   9296  Z= 0.307
  Chirality :  0.044   0.227   1036
  Planarity :  0.004   0.040   1194
  Dihedral  :  4.107  20.128    891
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.55 %
    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:  0.48 (0.29), residues: 822
  helix:  1.95 (0.28), residues: 360
  sheet: -0.62 (0.59), residues: 72
  loop : -1.09 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A 706 
 HIS   0.005   0.002   HIS A 223 
 PHE   0.014   0.002   PHE A 354 
 TYR   0.014   0.002   TYR A 384 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  301)
  hydrogen bonds       : angle       4.08641 (  873)
  SS BOND              : bond        0.00790 (    1)
  SS BOND              : angle       1.94232 (    2)
  covalent geometry    : bond        0.00477 ( 6862)
  covalent geometry    : angle       0.61004 ( 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: 26
    poor density    : 86
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8469 (m-40) cc_final: 0.8165 (m110)
REVERT: A  312 TYR cc_start: 0.8648 (t80) cc_final: 0.8374 (t80)
REVERT: A  456 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7706 (mtpp)
REVERT: A  801 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6597 (mm)
  outliers start: 26
  outliers final: 23
  residues processed: 107
  average time/residue: 0.1637
  time to fit residues: 24.8546
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  350 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  519 ASN
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  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  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:    0.9990
   chunk 78 optimal weight:    0.0570
   chunk 81 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 82 optimal weight:    0.3980
   chunk 53 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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
A 642 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.158714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133237 restraints weight = 10666.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.137415 restraints weight = 6382.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140233 restraints weight = 4497.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6863  Z= 0.107
  Angle     :  0.551   9.983   9296  Z= 0.276
  Chirality :  0.042   0.222   1036
  Planarity :  0.003   0.038   1194
  Dihedral  :  3.824  16.912    891
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.49 %
    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:  0.75 (0.29), residues: 822
  helix:  2.25 (0.28), residues: 359
  sheet: -0.55 (0.58), residues: 72
  loop : -1.02 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 706 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.014   0.001   PHE A 366 
 TYR   0.012   0.001   TYR A 856 
 ARG   0.002   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  301)
  hydrogen bonds       : angle       3.91673 (  873)
  SS BOND              : bond        0.00668 (    1)
  SS BOND              : angle       1.84901 (    2)
  covalent geometry    : bond        0.00242 ( 6862)
  covalent geometry    : angle       0.55024 ( 9294)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2419.35 seconds
wall clock time: 43 minutes 10.41 seconds (2590.41 seconds total)