Starting phenix.real_space_refine
on Wed Sep 17 05:44:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xnb_38500/09_2025/8xnb_38500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xnb_38500/09_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_38500/09_2025/8xnb_38500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xnb_38500/09_2025/8xnb_38500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xnb_38500/09_2025/8xnb_38500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xnb_38500/09_2025/8xnb_38500.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.69, per 1000 atoms: 0.30
  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: 0.53
  Conformation dependent library (CDL) restraints added in 241.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.20
  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: 0.96

  Time building geometry restraints manager: 0.72 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: 0.01
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:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.110
  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:1.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.620
-------------------------------------------------------------------------------
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= 0.211
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG B 551 
 TYR   0.026   0.002   TYR A 826 
 PHE   0.012   0.001   PHE B 812 
 TRP   0.017   0.002   TRP B 846 
 HIS   0.015   0.005   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 5712)
  covalent geometry    : angle       0.88542 ( 7752)
  hydrogen bonds       : bond        0.12967 (  338)
  hydrogen bonds       : angle       6.26089 (  942)

*********************** 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  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8469 (m-30) cc_final: 0.8256 (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: 0.0918
  time to fit residues: 15.4190
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  : 0.208 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** 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 = 0.3943 r_free = 0.3943 target = 0.173274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.125879 restraints weight = 7255.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.127053 restraints weight = 4143.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.128784 restraints weight = 3634.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.129226 restraints weight = 3281.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.129684 restraints weight = 2946.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   5712  Z= 0.279
  Angle     :  0.746   8.621   7752  Z= 0.397
  Chirality :  0.046   0.160    794
  Planarity :  0.005   0.041   1050
  Dihedral  :  5.976  30.085    826
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 27.16 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.28), residues: 734
  helix: -1.86 (0.77), residues: 18
  sheet:  0.11 (0.24), residues: 366
  loop : -2.61 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 578 
 TYR   0.021   0.002   TYR A 580 
 PHE   0.019   0.002   PHE B 796 
 TRP   0.018   0.003   TRP B 846 
 HIS   0.017   0.006   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 5712)
  covalent geometry    : angle       0.74623 ( 7752)
  hydrogen bonds       : bond        0.03820 (  338)
  hydrogen bonds       : angle       5.69600 (  942)

*********************** 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
  150 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 109
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8597 (m-30) cc_final: 0.8209 (m-30)
REVERT: A  706 GLU cc_start: 0.8939 (pt0) cc_final: 0.8683 (pt0)
REVERT: A  710 GLN cc_start: 0.5951 (tp40) cc_final: 0.5680 (mm-40)
REVERT: B  706 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8500 (pt0)
REVERT: B  710 GLN cc_start: 0.5921 (tp40) cc_final: 0.5647 (mm-40)
  outliers start: 41
  outliers final: 33
  residues processed: 128
  average time/residue: 0.0992
  time to fit residues: 15.9051
Evaluate side-chains
  140 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  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  718 THR
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 67 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0970
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** 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 = 0.4023 r_free = 0.4023 target = 0.181529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.129978 restraints weight = 7138.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.134566 restraints weight = 4124.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.137500 restraints weight = 3065.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.138845 restraints weight = 2604.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140180 restraints weight = 2393.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5712  Z= 0.120
  Angle     :  0.647  10.637   7752  Z= 0.338
  Chirality :  0.044   0.162    794
  Planarity :  0.004   0.037   1050
  Dihedral  :  5.362  21.857    826
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 30.40 %
    Favored  : 65.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.28), residues: 734
  helix: -1.23 (0.94), residues: 18
  sheet:  0.09 (0.24), residues: 366
  loop : -2.49 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 578 
 TYR   0.008   0.001   TYR A 580 
 PHE   0.011   0.001   PHE A 796 
 TRP   0.012   0.002   TRP B 790 
 HIS   0.007   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5712)
  covalent geometry    : angle       0.64665 ( 7752)
  hydrogen bonds       : bond        0.03141 (  338)
  hydrogen bonds       : angle       5.26654 (  942)

*********************** 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
  172 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 HIS cc_start: 0.7959 (m90) cc_final: 0.7753 (m90)
REVERT: A  537 ILE cc_start: 0.9239 (mm) cc_final: 0.8666 (mm)
REVERT: A  541 ASP cc_start: 0.8354 (m-30) cc_final: 0.8054 (m-30)
REVERT: A  543 ASP cc_start: 0.7225 (m-30) cc_final: 0.6774 (m-30)
REVERT: A  800 TYR cc_start: 0.6385 (m-10) cc_final: 0.5928 (m-10)
REVERT: B  706 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (pt0)
REVERT: B  800 TYR cc_start: 0.6397 (m-10) cc_final: 0.5945 (m-10)
  outliers start: 25
  outliers final: 21
  residues processed: 156
  average time/residue: 0.0888
  time to fit residues: 17.6620
Evaluate side-chains
  158 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  551 ARG
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  653 ASP
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  503 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  605 VAL
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  699 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 13 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0870
   chunk 5 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 512 HIS ** 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 = 0.4037 r_free = 0.4037 target = 0.182347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.131478 restraints weight = 7047.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.135832 restraints weight = 4108.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.138836 restraints weight = 3046.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.140651 restraints weight = 2578.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.141089 restraints weight = 2347.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5712  Z= 0.123
  Angle     :  0.672  12.107   7752  Z= 0.351
  Chirality :  0.043   0.164    794
  Planarity :  0.004   0.037   1050
  Dihedral  :  5.147  23.694    824
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 31.29 %
    Favored  : 64.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.28), residues: 734
  helix: -0.94 (1.01), residues: 18
  sheet: -0.02 (0.24), residues: 390
  loop : -2.50 (0.29), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 551 
 TYR   0.014   0.001   TYR B 502 
 PHE   0.008   0.001   PHE A 812 
 TRP   0.013   0.002   TRP B 790 
 HIS   0.009   0.002   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5712)
  covalent geometry    : angle       0.67199 ( 7752)
  hydrogen bonds       : bond        0.03025 (  338)
  hydrogen bonds       : angle       5.18652 (  942)

*********************** 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: 26
    poor density    : 140
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 HIS cc_start: 0.8136 (m-70) cc_final: 0.7637 (m90)
REVERT: A  537 ILE cc_start: 0.9272 (mm) cc_final: 0.8904 (mm)
REVERT: A  541 ASP cc_start: 0.8312 (m-30) cc_final: 0.8010 (m-30)
REVERT: A  543 ASP cc_start: 0.7230 (m-30) cc_final: 0.6805 (m-30)
REVERT: A  800 TYR cc_start: 0.6360 (m-10) cc_final: 0.5858 (m-10)
REVERT: B  800 TYR cc_start: 0.6365 (m-10) cc_final: 0.5875 (m-10)
  outliers start: 26
  outliers final: 13
  residues processed: 151
  average time/residue: 0.0885
  time to fit residues: 16.9223
Evaluate side-chains
  143 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  551 ARG
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  749 ASP
Chi-restraints excluded: chain B residue  536 THR
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  749 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    2.3984

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.175384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126176 restraints weight = 7263.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.130267 restraints weight = 5319.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.131267 restraints weight = 3612.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.131473 restraints weight = 3410.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.132396 restraints weight = 3034.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   5712  Z= 0.235
  Angle     :  0.747  14.996   7752  Z= 0.383
  Chirality :  0.045   0.157    794
  Planarity :  0.005   0.037   1050
  Dihedral  :  5.455  23.108    824
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 31.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.28), residues: 734
  helix: -1.30 (1.01), residues: 18
  sheet: -0.09 (0.24), residues: 386
  loop : -2.58 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 765 
 TYR   0.020   0.002   TYR A 580 
 PHE   0.013   0.002   PHE A 796 
 TRP   0.016   0.003   TRP B 846 
 HIS   0.008   0.003   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 5712)
  covalent geometry    : angle       0.74688 ( 7752)
  hydrogen bonds       : bond        0.03282 (  338)
  hydrogen bonds       : angle       5.47366 (  942)

*********************** 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
  154 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  541 ASP cc_start: 0.8495 (m-30) cc_final: 0.8063 (m-30)
REVERT: A  543 ASP cc_start: 0.7546 (m-30) cc_final: 0.6956 (m-30)
REVERT: A  706 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8103 (tp30)
REVERT: A  800 TYR cc_start: 0.6500 (m-10) cc_final: 0.6016 (m-10)
REVERT: A  810 LEU cc_start: 0.8185 (mt) cc_final: 0.7845 (mt)
REVERT: B  674 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6172 (ptp-170)
REVERT: B  710 GLN cc_start: 0.6074 (tp40) cc_final: 0.5793 (mm-40)
REVERT: B  800 TYR cc_start: 0.6499 (m-10) cc_final: 0.6009 (m-10)
  outliers start: 34
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0706
  time to fit residues: 12.7695
Evaluate side-chains
  145 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  551 ARG
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  687 ILE
Chi-restraints excluded: chain A residue  706 GLU
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  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  789 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0070
   chunk 35 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0670
   chunk 58 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 512 HIS
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.183210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.136101 restraints weight = 7094.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.137670 restraints weight = 3994.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.139326 restraints weight = 3468.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.140553 restraints weight = 3238.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.140298 restraints weight = 2832.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5712  Z= 0.117
  Angle     :  0.673  13.715   7752  Z= 0.342
  Chirality :  0.043   0.174    794
  Planarity :  0.004   0.037   1050
  Dihedral  :  5.077  22.406    824
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 33.27 %
    Favored  : 62.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.29), residues: 734
  helix: -0.95 (1.04), residues: 18
  sheet: -0.08 (0.25), residues: 382
  loop : -2.48 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 578 
 TYR   0.007   0.001   TYR A 502 
 PHE   0.009   0.001   PHE B 812 
 TRP   0.015   0.002   TRP B 790 
 HIS   0.008   0.002   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5712)
  covalent geometry    : angle       0.67332 ( 7752)
  hydrogen bonds       : bond        0.02817 (  338)
  hydrogen bonds       : angle       5.18436 (  942)

*********************** 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
  174 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 HIS cc_start: 0.7172 (m170) cc_final: 0.6919 (m-70)
REVERT: A  543 ASP cc_start: 0.7331 (m-30) cc_final: 0.6780 (m-30)
REVERT: A  706 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8064 (tp30)
REVERT: A  783 PHE cc_start: 0.8335 (p90) cc_final: 0.7881 (p90)
REVERT: A  800 TYR cc_start: 0.6232 (m-10) cc_final: 0.5790 (m-80)
REVERT: A  810 LEU cc_start: 0.8163 (mt) cc_final: 0.7809 (mt)
REVERT: B  512 HIS cc_start: 0.6790 (m170) cc_final: 0.6551 (m170)
REVERT: B  524 GLN cc_start: 0.7762 (pt0) cc_final: 0.7379 (pp30)
REVERT: B  751 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: B  783 PHE cc_start: 0.8372 (p90) cc_final: 0.7971 (p90)
REVERT: B  800 TYR cc_start: 0.6211 (m-10) cc_final: 0.5759 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 158
  average time/residue: 0.0871
  time to fit residues: 17.4941
Evaluate side-chains
  152 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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  551 ARG
Chi-restraints excluded: chain A residue  555 SER
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  672 VAL
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.172840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120226 restraints weight = 7340.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124396 restraints weight = 4345.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.127011 restraints weight = 3271.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128662 restraints weight = 2803.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.128756 restraints weight = 2574.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   5712  Z= 0.296
  Angle     :  0.746  12.076   7752  Z= 0.392
  Chirality :  0.045   0.176    794
  Planarity :  0.005   0.034   1050
  Dihedral  :  5.583  22.927    824
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 32.37 %
    Favored  : 61.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.28), residues: 734
  helix: -1.38 (1.11), residues: 18
  sheet: -0.12 (0.24), residues: 386
  loop : -2.66 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 765 
 TYR   0.022   0.002   TYR B 580 
 PHE   0.012   0.002   PHE B 556 
 TRP   0.018   0.003   TRP A 846 
 HIS   0.005   0.001   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 5712)
  covalent geometry    : angle       0.74643 ( 7752)
  hydrogen bonds       : bond        0.03396 (  338)
  hydrogen bonds       : angle       5.62126 (  942)

*********************** 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
  145 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  543 ASP cc_start: 0.7470 (m-30) cc_final: 0.6883 (m-30)
REVERT: A  706 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8002 (tp30)
REVERT: A  800 TYR cc_start: 0.6531 (m-10) cc_final: 0.6044 (m-10)
REVERT: B  485 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7902 (tt)
REVERT: B  512 HIS cc_start: 0.7668 (m170) cc_final: 0.7175 (m170)
REVERT: B  706 GLU cc_start: 0.8758 (pt0) cc_final: 0.8355 (pm20)
REVERT: B  800 TYR cc_start: 0.6512 (m-10) cc_final: 0.6031 (m-10)
  outliers start: 34
  outliers final: 26
  residues processed: 130
  average time/residue: 0.0772
  time to fit residues: 13.1085
Evaluate side-chains
  136 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  551 ARG
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  662 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  706 GLU
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  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  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  798 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 59 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0970
   chunk 50 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 550 ASN
** A 671 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.180283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.132051 restraints weight = 7072.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.136072 restraints weight = 5145.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.136651 restraints weight = 3549.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136943 restraints weight = 3171.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.139470 restraints weight = 3070.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5712  Z= 0.131
  Angle     :  0.687  11.830   7752  Z= 0.352
  Chirality :  0.044   0.156    794
  Planarity :  0.004   0.037   1050
  Dihedral  :  5.219  20.998    824
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 35.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.28), residues: 734
  helix: -1.09 (1.08), residues: 18
  sheet: -0.20 (0.24), residues: 382
  loop : -2.55 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 837 
 TYR   0.010   0.001   TYR A 731 
 PHE   0.015   0.001   PHE A 796 
 TRP   0.013   0.002   TRP B 790 
 HIS   0.010   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5712)
  covalent geometry    : angle       0.68702 ( 7752)
  hydrogen bonds       : bond        0.02889 (  338)
  hydrogen bonds       : angle       5.31698 (  942)

*********************** 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
  154 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 HIS cc_start: 0.7199 (m170) cc_final: 0.6615 (m170)
REVERT: A  543 ASP cc_start: 0.7226 (m-30) cc_final: 0.6667 (m-30)
REVERT: A  706 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7986 (tp30)
REVERT: A  783 PHE cc_start: 0.8400 (p90) cc_final: 0.8092 (p90)
REVERT: A  800 TYR cc_start: 0.6242 (m-10) cc_final: 0.5790 (m-80)
REVERT: B  512 HIS cc_start: 0.7076 (m170) cc_final: 0.6677 (m170)
REVERT: B  674 ARG cc_start: 0.6867 (tpp80) cc_final: 0.6109 (ptp-170)
REVERT: B  706 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (pm20)
REVERT: B  783 PHE cc_start: 0.8423 (p90) cc_final: 0.8123 (p90)
REVERT: B  800 TYR cc_start: 0.6242 (m-10) cc_final: 0.5714 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0787
  time to fit residues: 14.3710
Evaluate side-chains
  142 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  551 ARG
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  706 GLU
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  706 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.171324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.122813 restraints weight = 7275.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.127436 restraints weight = 5369.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.129137 restraints weight = 3451.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.129041 restraints weight = 3036.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.129540 restraints weight = 2834.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066   5712  Z= 0.309
  Angle     :  0.758  10.826   7752  Z= 0.399
  Chirality :  0.046   0.157    794
  Planarity :  0.005   0.034   1050
  Dihedral  :  5.796  28.176    824
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 33.45 %
    Favored  : 61.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.28), residues: 734
  helix: -1.49 (1.11), residues: 18
  sheet: -0.18 (0.24), residues: 386
  loop : -2.72 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 765 
 TYR   0.022   0.002   TYR B 580 
 PHE   0.015   0.002   PHE A 796 
 TRP   0.020   0.004   TRP A 846 
 HIS   0.010   0.003   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 ( 5712)
  covalent geometry    : angle       0.75756 ( 7752)
  hydrogen bonds       : bond        0.03366 (  338)
  hydrogen bonds       : angle       5.72044 (  942)

*********************** 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
  140 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: A  512 HIS cc_start: 0.7882 (m170) cc_final: 0.7263 (m-70)
REVERT: A  543 ASP cc_start: 0.7220 (m-30) cc_final: 0.6647 (m-30)
REVERT: A  706 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7990 (tp30)
REVERT: A  800 TYR cc_start: 0.6729 (m-10) cc_final: 0.6264 (m-10)
REVERT: B  485 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: B  674 ARG cc_start: 0.7084 (tpp80) cc_final: 0.6334 (ptp-170)
REVERT: B  706 GLU cc_start: 0.8773 (pt0) cc_final: 0.8395 (pm20)
REVERT: B  800 TYR cc_start: 0.6681 (m-10) cc_final: 0.6158 (m-10)
  outliers start: 27
  outliers final: 23
  residues processed: 129
  average time/residue: 0.0853
  time to fit residues: 14.1832
Evaluate side-chains
  137 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  551 ARG
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  662 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  776 GLN
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain A residue  798 SER
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  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  647 LEU
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  672 VAL
Chi-restraints excluded: chain B residue  789 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 ASN ** 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 = 0.4000 r_free = 0.4000 target = 0.177912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.129553 restraints weight = 7304.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.133519 restraints weight = 5306.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.134126 restraints weight = 3549.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135643 restraints weight = 3201.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135697 restraints weight = 2901.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2326

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= 0.146
  Angle     :  0.684  10.807   7752  Z= 0.355
  Chirality :  0.044   0.160    794
  Planarity :  0.004   0.036   1050
  Dihedral  :  5.429  25.403    824
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 34.71 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.28), residues: 734
  helix: -1.17 (1.10), residues: 18
  sheet: -0.29 (0.24), residues: 382
  loop : -2.61 (0.28), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 593 
 TYR   0.016   0.001   TYR B 502 
 PHE   0.012   0.001   PHE A 796 
 TRP   0.014   0.002   TRP A 846 
 HIS   0.005   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5712)
  covalent geometry    : angle       0.68413 ( 7752)
  hydrogen bonds       : bond        0.02930 (  338)
  hydrogen bonds       : angle       5.42193 (  942)

********************** 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
  147 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7720 (tt)
REVERT: A  512 HIS cc_start: 0.7170 (m170) cc_final: 0.6573 (m170)
REVERT: A  543 ASP cc_start: 0.7409 (m-30) cc_final: 0.6787 (m-30)
REVERT: A  674 ARG cc_start: 0.7033 (tpp80) cc_final: 0.6127 (ptp-170)
REVERT: A  706 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7954 (tp30)
REVERT: A  731 TYR cc_start: 0.8716 (m-80) cc_final: 0.8497 (m-80)
REVERT: A  783 PHE cc_start: 0.8464 (p90) cc_final: 0.8225 (p90)
REVERT: A  800 TYR cc_start: 0.6519 (m-10) cc_final: 0.6069 (m-80)
REVERT: B  512 HIS cc_start: 0.7242 (m170) cc_final: 0.6899 (m170)
REVERT: B  674 ARG cc_start: 0.7186 (tpp80) cc_final: 0.6254 (ptp-170)
REVERT: B  706 GLU cc_start: 0.8735 (pt0) cc_final: 0.8422 (pm20)
REVERT: B  800 TYR cc_start: 0.6430 (m-10) cc_final: 0.5887 (m-10)
  outliers start: 19
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0737
  time to fit residues: 13.2378
Evaluate side-chains
  144 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  551 ARG
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  662 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  776 GLN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.171280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.123177 restraints weight = 7255.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.127307 restraints weight = 5422.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.128266 restraints weight = 3623.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128466 restraints weight = 3453.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.129404 restraints weight = 3065.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   5712  Z= 0.294
  Angle     :  0.753  10.192   7752  Z= 0.399
  Chirality :  0.046   0.145    794
  Planarity :  0.005   0.035   1050
  Dihedral  :  5.860  28.714    824
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 34.35 %
    Favored  : 61.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.28), residues: 734
  helix: -1.31 (1.15), residues: 18
  sheet: -0.23 (0.25), residues: 386
  loop : -2.73 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 765 
 TYR   0.021   0.002   TYR B 580 
 PHE   0.065   0.002   PHE B 783 
 TRP   0.019   0.004   TRP A 846 
 HIS   0.011   0.003   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 5712)
  covalent geometry    : angle       0.75280 ( 7752)
  hydrogen bonds       : bond        0.03373 (  338)
  hydrogen bonds       : angle       5.74374 (  942)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1083.72 seconds
wall clock time: 19 minutes 24.47 seconds (1164.47 seconds total)