Starting phenix.real_space_refine
on Thu Mar  6 08:17:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xnb_38500/03_2025/8xnb_38500.cif"
  }
  resolution = 3.8
  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=   0.009 sd=   0.123
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: 3
    Type Number    sf(0)   Gaussians
     C    3498      2.51       5
     N     990      2.21       5
     O    1092      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5580
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2790
          Classifications: {'peptide': 369}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 357}
    Chain: "B"
      Number of atoms: 2790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2790
          Classifications: {'peptide': 369}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 357}
  Time building chain proxies: 3.59, per 1000 atoms: 0.64
  Number of scatterers: 5580
  At special positions: 0
  Unit cell: (90.95, 93.09, 78.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1092      8.00
     N     990      7.00
     C    3498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 656.6 milliseconds
  

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1232

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      3.8% alpha, 49.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 626 through 634
    Processing helix  chain 'A' and resid 739 through 743
      removed outlier: 3.803A  pdb=" N   GLU A 743 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 634
    Processing helix  chain 'B' and resid 739 through 743
      removed outlier: 3.814A  pdb=" N   GLU B 743 " --> pdb=" O   ALA B 740 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 484 through 490
      removed outlier: 3.756A  pdb=" N   ASN A 484 " --> pdb=" O   ALA A 501 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   ASP A 490 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   GLY A 495 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
      removed outlier: 9.294A  pdb=" N   TRP A 529 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A 562 " --> pdb=" O   TRP A 529 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ASN A 565 " --> pdb=" O   TYR A 580 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   TYR A 580 " --> pdb=" O   ASN A 565 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLN A 710 " --> pdb=" O   PHE A 695 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU A 778 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 699 through 700
    Processing sheet with id=AA3, first strand: chain 'A' and resid 731 through 733
    Processing sheet with id=AA4, first strand: chain 'B' and resid 484 through 490
      removed outlier: 3.762A  pdb=" N   ASN B 484 " --> pdb=" O   ALA B 501 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ASP B 490 " --> pdb=" O   GLY B 495 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLY B 495 " --> pdb=" O   ASP B 490 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   TRP B 529 " --> pdb=" O   VAL B 562 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B 562 " --> pdb=" O   TRP B 529 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASN B 565 " --> pdb=" O   TYR B 580 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   TYR B 580 " --> pdb=" O   ASN B 565 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLN B 710 " --> pdb=" O   PHE B 695 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LEU B 778 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 699 through 700
    Processing sheet with id=AA6, first strand: chain 'B' and resid 731 through 733

    338 hydrogen bonds defined for protein.
    942 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: 1.76

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.31: 944
        1.31 -     1.40: 1599
        1.40 -     1.48: 961
        1.48 -     1.57: 2206
        1.57 -     1.65: 2
  Bond restraints: 5712
  Sorted by residual:
  bond pdb=" CB  PRO A 679 "
       pdb=" CG  PRO A 679 "
    ideal  model  delta    sigma   weight residual
    1.492  1.652 -0.160 5.00e-02 4.00e+02 1.03e+01
  bond pdb=" CB  PRO B 679 "
       pdb=" CG  PRO B 679 "
    ideal  model  delta    sigma   weight residual
    1.492  1.650 -0.158 5.00e-02 4.00e+02 9.97e+00
  bond pdb=" CB  LYS B 549 "
       pdb=" CG  LYS B 549 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.21e+00
  bond pdb=" CB  ASP A 546 "
       pdb=" CG  ASP A 546 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.19e+00
  bond pdb=" C   ILE B 481 "
       pdb=" N   PRO B 482 "
    ideal  model  delta    sigma   weight residual
    1.335  1.323  0.012 8.70e-03 1.32e+04 1.98e+00
  ... (remaining 5707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 7662
        3.26 -     6.52: 76
        6.52 -     9.77: 8
        9.77 -    13.03: 2
       13.03 -    16.29: 4
  Bond angle restraints: 7752
  Sorted by residual:
  angle pdb=" CA  PRO A 679 "
        pdb=" N   PRO A 679 "
        pdb=" CD  PRO A 679 "
      ideal   model   delta    sigma   weight residual
     112.00  101.70   10.30 1.40e+00 5.10e-01 5.42e+01
  angle pdb=" CA  PRO B 679 "
        pdb=" N   PRO B 679 "
        pdb=" CD  PRO B 679 "
      ideal   model   delta    sigma   weight residual
     112.00  102.09    9.91 1.40e+00 5.10e-01 5.01e+01
  angle pdb=" CA  LEU B 705 "
        pdb=" CB  LEU B 705 "
        pdb=" CG  LEU B 705 "
      ideal   model   delta    sigma   weight residual
     116.30  132.59  -16.29 3.50e+00 8.16e-02 2.17e+01
  angle pdb=" CA  LEU A 705 "
        pdb=" CB  LEU A 705 "
        pdb=" CG  LEU A 705 "
      ideal   model   delta    sigma   weight residual
     116.30  132.47  -16.17 3.50e+00 8.16e-02 2.13e+01
  angle pdb=" CA  LEU A 510 "
        pdb=" CB  LEU A 510 "
        pdb=" CG  LEU A 510 "
      ideal   model   delta    sigma   weight residual
     116.30  131.98  -15.68 3.50e+00 8.16e-02 2.01e+01
  ... (remaining 7747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 2702
       16.69 -    33.38: 361
       33.38 -    50.07: 114
       50.07 -    66.77: 21
       66.77 -    83.46: 4
  Dihedral angle restraints: 3202
    sinusoidal: 1194
      harmonic: 2008
  Sorted by residual:
  dihedral pdb=" CA  LYS B 700 "
           pdb=" C   LYS B 700 "
           pdb=" N   ARG B 701 "
           pdb=" CA  ARG B 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.47   23.53     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A 700 "
           pdb=" C   LYS A 700 "
           pdb=" N   ARG A 701 "
           pdb=" CA  ARG A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.61   23.39     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  GLU B 763 "
           pdb=" C   GLU B 763 "
           pdb=" N   TYR B 764 "
           pdb=" CA  TYR B 764 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 3199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 546
       0.041 -    0.082: 178
       0.082 -    0.123: 58
       0.123 -    0.164: 5
       0.164 -    0.205: 7
  Chirality restraints: 794
  Sorted by residual:
  chirality pdb=" CA  PRO A 679 "
            pdb=" N   PRO A 679 "
            pdb=" C   PRO A 679 "
            pdb=" CB  PRO A 679 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  PRO B 679 "
            pdb=" N   PRO B 679 "
            pdb=" C   PRO B 679 "
            pdb=" CB  PRO B 679 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  ILE A 537 "
            pdb=" N   ILE A 537 "
            pdb=" C   ILE A 537 "
            pdb=" CB  ILE A 537 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.72e-01
  ... (remaining 791 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 678 "    0.060 5.00e-02 4.00e+02   8.50e-02 1.16e+01
        pdb=" N   PRO A 679 "   -0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 679 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 679 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 678 "   -0.059 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO B 679 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 679 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 679 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 826 "    0.008 2.00e-02 2.50e+03   1.07e-02 2.28e+00
        pdb=" CG  TYR A 826 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 826 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 826 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 826 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 826 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 826 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 826 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 274
        2.71 -     3.26: 5351
        3.26 -     3.81: 8596
        3.81 -     4.35: 9833
        4.35 -     4.90: 18037
  Nonbonded interactions: 42091
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 844 "
            pdb=" N   PHE A 845 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OD1 ASN B 844 "
            pdb=" N   PHE B 845 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   ASP A 627 "
            pdb=" OG1 THR A 631 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N   ARG A 478 "
            pdb=" O   GLN B 816 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   GLN A 816 "
            pdb=" N   ARG B 478 "
     model   vdw
     2.204 3.120
  ... (remaining 42086 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.450
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
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      :  0.005   0.160   5712  Z= 0.305
  Angle     :  0.885  16.291   7752  Z= 0.461
  Chirality :  0.047   0.205    794
  Planarity :  0.005   0.085   1050
  Dihedral  : 16.785  83.457   1970
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 33.45 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.28), residues: 734
  helix: -1.46 (0.93), residues: 18
  sheet:  0.26 (0.25), residues: 370
  loop : -2.58 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 846 
 HIS   0.015   0.005   HIS A 512 
 PHE   0.012   0.001   PHE B 812 
 TYR   0.026   0.002   TYR A 826 
 ARG   0.004   0.000   ARG B 551 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 133
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8469 (m-30) cc_final: 0.8254 (m-30)
REVERT: B  512 HIS cc_start: 0.7424 (m90) cc_final: 0.6809 (m-70)
  outliers start: 3
  outliers final: 2
  residues processed: 133
  average time/residue: 0.1906
  time to fit residues: 32.1379
Evaluate side-chains
  118 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 56 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 ASN
B 504 ASN
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.169757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122185 restraints weight = 7273.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.123327 restraints weight = 4451.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.124257 restraints weight = 3707.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074   5712  Z= 0.521
  Angle     :  0.814   8.167   7752  Z= 0.439
  Chirality :  0.048   0.159    794
  Planarity :  0.006   0.048   1050
  Dihedral  :  6.320  33.486    826
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  8.99 %
    Allowed  : 26.26 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.28), residues: 734
  helix: -2.09 (0.76), residues: 18
  sheet:  0.09 (0.25), residues: 366
  loop : -2.67 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP A 846 
 HIS   0.019   0.007   HIS A 512 
 PHE   0.022   0.003   PHE A 796 
 TYR   0.026   0.002   TYR A 580 
 ARG   0.009   0.001   ARG A 674 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 105
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  674 ARG cc_start: 0.6553 (tpp80) cc_final: 0.6153 (tpp80)
REVERT: A  706 GLU cc_start: 0.8967 (pt0) cc_final: 0.8521 (pm20)
REVERT: B  485 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7709 (tt)
REVERT: B  706 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8530 (pt0)
REVERT: B  763 GLU cc_start: 0.8755 (pt0) cc_final: 0.8546 (pt0)
  outliers start: 50
  outliers final: 33
  residues processed: 130
  average time/residue: 0.1959
  time to fit residues: 32.0906
Evaluate side-chains
  136 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  543 ASP
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  711 VAL
Chi-restraints excluded: chain B residue  765 ARG
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.176313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.127915 restraints weight = 7275.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.132869 restraints weight = 5157.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.134642 restraints weight = 3265.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5712  Z= 0.217
  Angle     :  0.656   5.887   7752  Z= 0.349
  Chirality :  0.044   0.170    794
  Planarity :  0.004   0.035   1050
  Dihedral  :  5.655  25.776    826
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.40 %
    Favored  : 64.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.28), residues: 734
  helix: -1.65 (0.93), residues: 18
  sheet:  0.03 (0.24), residues: 366
  loop : -2.59 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 846 
 HIS   0.008   0.003   HIS A 512 
 PHE   0.015   0.001   PHE B 796 
 TYR   0.015   0.001   TYR A 826 
 ARG   0.006   0.001   ARG A 578 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8496 (m-30) cc_final: 0.8127 (m-30)
REVERT: A  543 ASP cc_start: 0.7679 (m-30) cc_final: 0.7061 (m-30)
REVERT: A  674 ARG cc_start: 0.6604 (tpp80) cc_final: 0.6280 (tpp80)
REVERT: A  800 TYR cc_start: 0.6491 (m-10) cc_final: 0.6063 (m-10)
REVERT: B  706 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8506 (pt0)
REVERT: B  800 TYR cc_start: 0.6526 (m-10) cc_final: 0.6088 (m-10)
  outliers start: 29
  outliers final: 22
  residues processed: 142
  average time/residue: 0.1916
  time to fit residues: 34.4281
Evaluate side-chains
  141 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  711 VAL
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  765 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.169389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.117701 restraints weight = 7420.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121569 restraints weight = 4371.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.124166 restraints weight = 3296.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   5712  Z= 0.429
  Angle     :  0.739  10.666   7752  Z= 0.398
  Chirality :  0.045   0.177    794
  Planarity :  0.005   0.038   1050
  Dihedral  :  5.891  27.583    824
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  9.71 %
    Allowed  : 27.70 %
    Favored  : 62.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.28), residues: 734
  helix: -1.80 (1.05), residues: 18
  sheet: -0.08 (0.25), residues: 386
  loop : -2.82 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 846 
 HIS   0.019   0.005   HIS B 512 
 PHE   0.013   0.002   PHE A 556 
 TYR   0.022   0.002   TYR A 580 
 ARG   0.006   0.001   ARG B 765 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 112
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8682 (m-30) cc_final: 0.8247 (m-30)
REVERT: A  543 ASP cc_start: 0.7587 (m-30) cc_final: 0.6874 (m-30)
REVERT: A  674 ARG cc_start: 0.6668 (tpp80) cc_final: 0.6264 (tpp80)
REVERT: A  779 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8184 (m-10)
REVERT: B  674 ARG cc_start: 0.6658 (tpp80) cc_final: 0.6305 (tpp80)
REVERT: B  779 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8145 (m-10)
  outliers start: 54
  outliers final: 38
  residues processed: 142
  average time/residue: 0.1885
  time to fit residues: 34.1726
Evaluate side-chains
  142 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 102
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  543 ASP
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  711 VAL
Chi-restraints excluded: chain B residue  762 LEU
Chi-restraints excluded: chain B residue  765 ARG
Chi-restraints excluded: chain B residue  779 TYR
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 HIS
** B 671 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 = 0.3962 r_free = 0.3962 target = 0.175469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.127217 restraints weight = 7281.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.128610 restraints weight = 5072.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.130447 restraints weight = 3770.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5712  Z= 0.219
  Angle     :  0.698  15.149   7752  Z= 0.356
  Chirality :  0.044   0.178    794
  Planarity :  0.004   0.034   1050
  Dihedral  :  5.507  21.466    824
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.94 %
    Favored  : 63.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.28), residues: 734
  helix: -1.80 (0.97), residues: 18
  sheet: -0.09 (0.25), residues: 386
  loop : -2.68 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 846 
 HIS   0.011   0.003   HIS B 512 
 PHE   0.011   0.001   PHE B 812 
 TYR   0.016   0.001   TYR A 826 
 ARG   0.004   0.000   ARG A 765 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8518 (m-30) cc_final: 0.8157 (m-30)
REVERT: A  543 ASP cc_start: 0.7602 (m-30) cc_final: 0.6868 (m-30)
REVERT: A  674 ARG cc_start: 0.6527 (tpp80) cc_final: 0.6061 (tpp80)
REVERT: A  706 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8292 (pm20)
REVERT: A  800 TYR cc_start: 0.6581 (m-10) cc_final: 0.6093 (m-10)
REVERT: B  674 ARG cc_start: 0.6566 (tpp80) cc_final: 0.6293 (tpp80)
REVERT: B  800 TYR cc_start: 0.6587 (m-10) cc_final: 0.6094 (m-10)
  outliers start: 29
  outliers final: 24
  residues processed: 144
  average time/residue: 0.1811
  time to fit residues: 33.7509
Evaluate side-chains
  151 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  765 ARG
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 69 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.171059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.122342 restraints weight = 7323.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.122801 restraints weight = 4470.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.123806 restraints weight = 4000.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   5712  Z= 0.358
  Angle     :  0.729  13.412   7752  Z= 0.380
  Chirality :  0.044   0.157    794
  Planarity :  0.005   0.034   1050
  Dihedral  :  5.724  25.700    824
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 29.50 %
    Favored  : 62.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.28), residues: 734
  helix: -1.93 (1.02), residues: 18
  sheet: -0.10 (0.25), residues: 390
  loop : -2.76 (0.28), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 846 
 HIS   0.020   0.006   HIS B 512 
 PHE   0.010   0.002   PHE A 812 
 TYR   0.021   0.002   TYR A 580 
 ARG   0.004   0.001   ARG A 765 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 119
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8633 (m-30) cc_final: 0.8258 (m-30)
REVERT: A  543 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.6725 (m-30)
REVERT: A  674 ARG cc_start: 0.6564 (tpp80) cc_final: 0.6082 (tpp80)
REVERT: A  706 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8312 (pm20)
REVERT: B  512 HIS cc_start: 0.7633 (m90) cc_final: 0.7432 (m90)
REVERT: B  674 ARG cc_start: 0.6603 (tpp80) cc_final: 0.6293 (tpp80)
REVERT: B  800 TYR cc_start: 0.6749 (m-10) cc_final: 0.6261 (m-10)
  outliers start: 43
  outliers final: 31
  residues processed: 137
  average time/residue: 0.1771
  time to fit residues: 31.1674
Evaluate side-chains
  147 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  543 ASP
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  762 LEU
Chi-restraints excluded: chain B residue  765 ARG
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.173876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125612 restraints weight = 7292.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.130289 restraints weight = 5434.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.131870 restraints weight = 3571.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5712  Z= 0.264
  Angle     :  0.690  12.385   7752  Z= 0.359
  Chirality :  0.044   0.160    794
  Planarity :  0.005   0.034   1050
  Dihedral  :  5.510  19.229    824
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 30.04 %
    Favored  : 62.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.28), residues: 734
  helix: -1.92 (0.99), residues: 18
  sheet: -0.13 (0.25), residues: 390
  loop : -2.70 (0.29), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 846 
 HIS   0.016   0.005   HIS B 512 
 PHE   0.011   0.002   PHE B 845 
 TYR   0.017   0.002   TYR B 580 
 ARG   0.004   0.000   ARG A 765 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8494 (m-30) cc_final: 0.8156 (m-30)
REVERT: A  543 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6685 (m-30)
REVERT: A  674 ARG cc_start: 0.6571 (tpp80) cc_final: 0.6151 (tpp80)
REVERT: A  706 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8297 (pm20)
REVERT: A  800 TYR cc_start: 0.6730 (m-10) cc_final: 0.6221 (m-10)
REVERT: B  485 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7702 (tt)
REVERT: B  674 ARG cc_start: 0.6605 (tpp80) cc_final: 0.6340 (tpp80)
REVERT: B  706 GLU cc_start: 0.8766 (pt0) cc_final: 0.8123 (tp30)
REVERT: B  800 TYR cc_start: 0.6658 (m-10) cc_final: 0.6130 (m-10)
REVERT: B  837 ARG cc_start: 0.7782 (ptt-90) cc_final: 0.7567 (ptt180)
  outliers start: 41
  outliers final: 30
  residues processed: 142
  average time/residue: 0.1831
  time to fit residues: 33.1904
Evaluate side-chains
  153 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  578 ARG
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  686 GLU
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  762 LEU
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0570
   chunk 62 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.3902

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.175310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127495 restraints weight = 7272.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.128626 restraints weight = 5161.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.129986 restraints weight = 3854.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5712  Z= 0.233
  Angle     :  0.685  13.406   7752  Z= 0.351
  Chirality :  0.044   0.159    794
  Planarity :  0.004   0.034   1050
  Dihedral  :  5.386  19.668    824
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 31.65 %
    Favored  : 62.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.28), residues: 734
  helix: -1.88 (0.97), residues: 18
  sheet: -0.13 (0.25), residues: 390
  loop : -2.73 (0.28), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 846 
 HIS   0.013   0.004   HIS A 512 
 PHE   0.009   0.001   PHE B 812 
 TYR   0.019   0.001   TYR A 826 
 ARG   0.005   0.000   ARG A 837 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.624 
Fit side-chains
REVERT: A  541 ASP cc_start: 0.8542 (m-30) cc_final: 0.8168 (m-30)
REVERT: A  543 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6747 (m-30)
REVERT: A  674 ARG cc_start: 0.6571 (tpp80) cc_final: 0.6144 (tpp80)
REVERT: A  706 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8271 (pm20)
REVERT: A  747 LEU cc_start: 0.8098 (mm) cc_final: 0.7724 (mm)
REVERT: A  748 GLU cc_start: 0.7467 (mp0) cc_final: 0.7196 (mp0)
REVERT: A  800 TYR cc_start: 0.6622 (m-10) cc_final: 0.6127 (m-10)
REVERT: B  485 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7753 (tt)
REVERT: B  674 ARG cc_start: 0.6615 (tpp80) cc_final: 0.6297 (tpp80)
REVERT: B  706 GLU cc_start: 0.8834 (pt0) cc_final: 0.8045 (tp30)
REVERT: B  800 TYR cc_start: 0.6623 (m-10) cc_final: 0.6107 (m-10)
  outliers start: 31
  outliers final: 26
  residues processed: 143
  average time/residue: 0.1667
  time to fit residues: 31.2029
Evaluate side-chains
  152 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  687 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  578 ARG
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  687 ILE
Chi-restraints excluded: chain B residue  762 LEU
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 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 = 0.4001 r_free = 0.4001 target = 0.178968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.131161 restraints weight = 7241.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.132304 restraints weight = 5012.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.133685 restraints weight = 3795.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5712  Z= 0.194
  Angle     :  0.666  13.719   7752  Z= 0.339
  Chirality :  0.043   0.165    794
  Planarity :  0.004   0.036   1050
  Dihedral  :  5.148  18.046    824
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 34.53 %
    Favored  : 61.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.28), residues: 734
  helix: -1.64 (0.96), residues: 18
  sheet: -0.16 (0.25), residues: 382
  loop : -2.64 (0.27), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 846 
 HIS   0.015   0.004   HIS A 512 
 PHE   0.009   0.001   PHE B 812 
 TYR   0.019   0.001   TYR A 826 
 ARG   0.002   0.000   ARG A 578 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8385 (m-30) cc_final: 0.8080 (m-30)
REVERT: A  543 ASP cc_start: 0.7493 (m-30) cc_final: 0.6731 (m-30)
REVERT: A  674 ARG cc_start: 0.6550 (tpp80) cc_final: 0.6115 (tpp80)
REVERT: A  706 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8261 (pm20)
REVERT: A  731 TYR cc_start: 0.8710 (m-80) cc_final: 0.8505 (m-80)
REVERT: A  800 TYR cc_start: 0.6522 (m-10) cc_final: 0.5974 (m-10)
REVERT: B  674 ARG cc_start: 0.6589 (tpp80) cc_final: 0.6276 (tpp80)
REVERT: B  706 GLU cc_start: 0.8760 (pt0) cc_final: 0.7958 (tp30)
REVERT: B  747 LEU cc_start: 0.7922 (mm) cc_final: 0.7552 (mm)
REVERT: B  800 TYR cc_start: 0.6416 (m-10) cc_final: 0.5928 (m-10)
  outliers start: 24
  outliers final: 18
  residues processed: 138
  average time/residue: 0.1622
  time to fit residues: 29.5149
Evaluate side-chains
  138 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  578 ARG
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  690 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    0.0060
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    3.1002

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.170382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122996 restraints weight = 7347.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124583 restraints weight = 4338.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125749 restraints weight = 3630.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   5712  Z= 0.410
  Angle     :  0.739  12.776   7752  Z= 0.386
  Chirality :  0.045   0.158    794
  Planarity :  0.005   0.033   1050
  Dihedral  :  5.662  27.011    824
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 34.53 %
    Favored  : 60.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.28), residues: 734
  helix: -1.77 (1.05), residues: 18
  sheet: -0.16 (0.25), residues: 390
  loop : -2.78 (0.28), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 846 
 HIS   0.018   0.005   HIS A 512 
 PHE   0.011   0.002   PHE B 822 
 TYR   0.023   0.002   TYR B 580 
 ARG   0.005   0.001   ARG A 745 

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8612 (m-30) cc_final: 0.8287 (m-30)
REVERT: A  543 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6700 (m-30)
REVERT: A  674 ARG cc_start: 0.6596 (tpp80) cc_final: 0.6213 (tpp80)
REVERT: A  706 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8261 (pm20)
REVERT: A  800 TYR cc_start: 0.6756 (m-10) cc_final: 0.6251 (m-10)
REVERT: B  674 ARG cc_start: 0.6606 (tpp80) cc_final: 0.6214 (tpp80)
REVERT: B  800 TYR cc_start: 0.6765 (m-10) cc_final: 0.6295 (m-10)
  outliers start: 25
  outliers final: 20
  residues processed: 127
  average time/residue: 0.1670
  time to fit residues: 28.0962
Evaluate side-chains
  136 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  543 ASP
Chi-restraints excluded: chain B residue  555 SER
Chi-restraints excluded: chain B residue  578 ARG
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  690 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   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 512 HIS
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 ASN
** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.176645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128985 restraints weight = 7381.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130955 restraints weight = 4350.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.131922 restraints weight = 3536.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5712  Z= 0.218
  Angle     :  0.675  13.194   7752  Z= 0.345
  Chirality :  0.044   0.169    794
  Planarity :  0.004   0.035   1050
  Dihedral  :  5.355  22.503    824
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 35.61 %
    Favored  : 60.61 %
  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: -2.00 (0.28), residues: 734
  helix: -1.69 (1.01), residues: 18
  sheet: -0.26 (0.25), residues: 386
  loop : -2.69 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 846 
 HIS   0.014   0.004   HIS A 512 
 PHE   0.009   0.001   PHE A 812 
 TYR   0.018   0.001   TYR A 826 
 ARG   0.002   0.000   ARG A 578 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1858.58 seconds
wall clock time: 32 minutes 57.25 seconds (1977.25 seconds total)