Starting phenix.real_space_refine
on Wed Sep 17 05:19:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw4_38730/09_2025/8xw4_38730.cif"
  }
  resolution = 3.84
  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=   0.003 sd=   0.068
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    3331      2.51       5
     N     810      2.21       5
     O     845      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 5027
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 5027
          Classifications: {'peptide': 619}
          Link IDs: {'PTRANS': 24, 'TRANS': 594}
          Chain breaks: 3
  Time building chain proxies: 1.67, per 1000 atoms: 0.33
  Number of scatterers: 5027
  At special positions: 0
  Unit cell: (90.47, 94.62, 99.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O     845      8.00
     N     810      7.00
     C    3331      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: 0.37
  Conformation dependent library (CDL) restraints added in 138.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1182

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      68.8% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 39
      removed outlier: 3.558A  pdb=" N   GLY A  39 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 36 through 39'
    Processing helix  chain 'A' and resid 40 through 67
      removed outlier: 3.844A  pdb=" N   VAL A  44 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 144
      removed outlier: 3.861A  pdb=" N   CYS A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 180
      removed outlier: 4.885A  pdb=" N   LEU A 174 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
      removed outlier: 3.690A  pdb=" N   GLY A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.779A  pdb=" N   ARG A 192 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 228
      removed outlier: 3.949A  pdb=" N   LEU A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
    Processing helix  chain 'A' and resid 277 through 305
    Processing helix  chain 'A' and resid 331 through 355
    Processing helix  chain 'A' and resid 368 through 379
      removed outlier: 3.619A  pdb=" N   PHE A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 457
      removed outlier: 4.175A  pdb=" N   CYS A 434 " --> pdb=" O   TRP A 430 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.203A  pdb=" N   PHE A 479 " --> pdb=" O   ILE A 475 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 506 through 527
    Processing helix  chain 'A' and resid 527 through 549
    Processing helix  chain 'A' and resid 556 through 560
      removed outlier: 3.667A  pdb=" N   CYS A 559 " --> pdb=" O   ARG A 556 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 560 " --> pdb=" O   PHE A 557 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 556 through 560'
    Processing helix  chain 'A' and resid 562 through 566
      removed outlier: 3.780A  pdb=" N   GLY A 566 " --> pdb=" O   PRO A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 586
      removed outlier: 4.099A  pdb=" N   MET A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 595
      removed outlier: 5.814A  pdb=" N   MET A 593 " --> pdb=" O   PRO A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 637
      removed outlier: 3.762A  pdb=" N   ALA A 623 " --> pdb=" O   GLN A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 667
      removed outlier: 4.584A  pdb=" N   PHE A 647 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 704
      removed outlier: 3.918A  pdb=" N   SER A 678 " --> pdb=" O   LYS A 674 " (cutoff:3.500A)
      Proline residue:  A 688  - end of helix
    Processing helix  chain 'A' and resid 707 through 730
      removed outlier: 3.587A  pdb=" N   HIS A 727 " --> pdb=" O   ILE A 723 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL A 728 " --> pdb=" O   CYS A 724 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   CYS A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 243

    309 hydrogen bonds defined for protein.
    918 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: 0.74

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1263
        1.33 -     1.45: 1024
        1.45 -     1.57: 2818
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 5165
  Sorted by residual:
  bond pdb=" CB  TRP A 694 "
       pdb=" CG  TRP A 694 "
    ideal  model  delta    sigma   weight residual
    1.498  1.449  0.049 3.10e-02 1.04e+03 2.47e+00
  bond pdb=" CB  MET A 628 "
       pdb=" CG  MET A 628 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.33e+00
  bond pdb=" CB  LEU A 445 "
       pdb=" CG  LEU A 445 "
    ideal  model  delta    sigma   weight residual
    1.530  1.501  0.029 2.00e-02 2.50e+03 2.04e+00
  bond pdb=" CB  GLN A 155 "
       pdb=" CG  GLN A 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.92e+00
  bond pdb=" C   ILE A 588 "
       pdb=" N   PRO A 589 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.88e+00
  ... (remaining 5160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 6763
        2.10 -     4.20: 201
        4.20 -     6.31: 34
        6.31 -     8.41: 6
        8.41 -    10.51: 2
  Bond angle restraints: 7006
  Sorted by residual:
  angle pdb=" C   ILE A 425 "
        pdb=" N   ARG A 426 "
        pdb=" CA  ARG A 426 "
      ideal   model   delta    sigma   weight residual
     120.89  128.04   -7.15 1.50e+00 4.44e-01 2.27e+01
  angle pdb=" CA  MET A 361 "
        pdb=" CB  MET A 361 "
        pdb=" CG  MET A 361 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CB  MET A 628 "
        pdb=" CG  MET A 628 "
        pdb=" SD  MET A 628 "
      ideal   model   delta    sigma   weight residual
     112.70  102.19   10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" N   ILE A 689 "
        pdb=" CA  ILE A 689 "
        pdb=" C   ILE A 689 "
      ideal   model   delta    sigma   weight residual
     110.72  107.20    3.52 1.01e+00 9.80e-01 1.21e+01
  angle pdb=" C   THR A 457 "
        pdb=" N   MET A 458 "
        pdb=" CA  MET A 458 "
      ideal   model   delta    sigma   weight residual
     121.64  114.49    7.15 2.13e+00 2.20e-01 1.13e+01
  ... (remaining 7001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 2673
       16.68 -    33.35: 260
       33.35 -    50.03: 78
       50.03 -    66.70: 5
       66.70 -    83.38: 5
  Dihedral angle restraints: 3021
    sinusoidal: 1195
      harmonic: 1826
  Sorted by residual:
  dihedral pdb=" CA  ALA A 412 "
           pdb=" C   ALA A 412 "
           pdb=" N   PRO A 413 "
           pdb=" CA  PRO A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.48  -36.52     0      5.00e+00 4.00e-02 5.33e+01
  dihedral pdb=" CA  MET A 282 "
           pdb=" C   MET A 282 "
           pdb=" N   PHE A 283 "
           pdb=" CA  PHE A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.61   24.39     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  GLU A 184 "
           pdb=" C   GLU A 184 "
           pdb=" N   ASN A 185 "
           pdb=" CA  ASN A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.60  -23.40     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 3018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 530
       0.042 -    0.084: 183
       0.084 -    0.125: 63
       0.125 -    0.167: 12
       0.167 -    0.209: 8
  Chirality restraints: 796
  Sorted by residual:
  chirality pdb=" CA  MET A 223 "
            pdb=" N   MET A 223 "
            pdb=" C   MET A 223 "
            pdb=" CB  MET A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  TRP A 694 "
            pdb=" N   TRP A 694 "
            pdb=" C   TRP A 694 "
            pdb=" CB  TRP A 694 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE A 474 "
            pdb=" CA  ILE A 474 "
            pdb=" CG1 ILE A 474 "
            pdb=" CG2 ILE A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.60e-01
  ... (remaining 793 not shown)

  Planarity restraints: 856
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 694 "   -0.034 2.00e-02 2.50e+03   2.55e-02 1.62e+01
        pdb=" CG  TRP A 694 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 694 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 694 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 694 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 694 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 694 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 694 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 694 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 694 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 407 "    0.027 2.00e-02 2.50e+03   2.17e-02 1.17e+01
        pdb=" CG  TRP A 407 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 407 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 407 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 407 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 407 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 407 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 407 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 407 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 407 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 197 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.34e+00
        pdb=" C   ASN A 197 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 197 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 198 "    0.012 2.00e-02 2.50e+03
  ... (remaining 853 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 12
        2.38 -     3.01: 3029
        3.01 -     3.64: 7579
        3.64 -     4.27: 10504
        4.27 -     4.90: 17189
  Nonbonded interactions: 38313
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 302 "
            pdb=" O   VAL A 307 "
     model   vdw
     1.751 3.120
  nonbonded pdb=" OE1 GLN A 302 "
            pdb=" N   VAL A 307 "
     model   vdw
     1.766 3.120
  nonbonded pdb=" OE1 GLN A 302 "
            pdb=" C   ASN A 306 "
     model   vdw
     2.056 3.270
  nonbonded pdb=" NE2 GLN A 302 "
            pdb=" C   VAL A 307 "
     model   vdw
     2.084 3.350
  nonbonded pdb=" O   LYS A 675 "
            pdb=" OG  SER A 678 "
     model   vdw
     2.252 3.040
  ... (remaining 38308 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     7.090
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
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      :  0.006   0.049   5165  Z= 0.266
  Angle     :  0.871  10.510   7006  Z= 0.481
  Chirality :  0.051   0.209    796
  Planarity :  0.005   0.041    856
  Dihedral  : 14.645  83.378   1839
  Min Nonbonded Distance : 1.751

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.80 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.84 (0.34), residues: 611
  helix:  0.88 (0.27), residues: 385
  sheet: -4.00 (0.92), residues: 12
  loop : -3.15 (0.38), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.028   0.002   TYR A 297 
 PHE   0.025   0.002   PHE A 705 
 TRP   0.068   0.004   TRP A 694 
 HIS   0.007   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 5165)
  covalent geometry    : angle       0.87088 ( 7006)
  hydrogen bonds       : bond        0.10823 (  309)
  hydrogen bonds       : angle       5.98189 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8804 (mm) cc_final: 0.8208 (tp)
REVERT: A  260 PHE cc_start: 0.8500 (m-10) cc_final: 0.8069 (m-80)
REVERT: A  292 GLU cc_start: 0.8936 (mp0) cc_final: 0.8562 (mp0)
REVERT: A  298 PHE cc_start: 0.9058 (m-10) cc_final: 0.8721 (m-10)
REVERT: A  349 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8610 (tpp80)
REVERT: A  361 MET cc_start: 0.7502 (mmp) cc_final: 0.6983 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0627
  time to fit residues: 9.8783
Evaluate side-chains
  87 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0470
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 GLN
A 571 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.175652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.121822 restraints weight = 7660.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.125715 restraints weight = 4132.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128155 restraints weight = 2973.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129444 restraints weight = 2490.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129713 restraints weight = 2262.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5165  Z= 0.148
  Angle     :  0.692   8.683   7006  Z= 0.355
  Chirality :  0.044   0.176    796
  Planarity :  0.005   0.047    856
  Dihedral  :  5.590  31.953    669
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.34 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.43 (0.35), residues: 611
  helix:  1.21 (0.27), residues: 380
  sheet: -3.01 (1.23), residues: 12
  loop : -2.97 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.017   0.002   TYR A 336 
 PHE   0.023   0.001   PHE A 712 
 TRP   0.044   0.003   TRP A 407 
 HIS   0.005   0.001   HIS A 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5165)
  covalent geometry    : angle       0.69173 ( 7006)
  hydrogen bonds       : bond        0.05336 (  309)
  hydrogen bonds       : angle       4.90828 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  244 ILE cc_start: 0.8815 (mm) cc_final: 0.8399 (tp)
REVERT: A  260 PHE cc_start: 0.8492 (m-10) cc_final: 0.8088 (m-80)
REVERT: A  282 MET cc_start: 0.8504 (ptt) cc_final: 0.8295 (ptm)
REVERT: A  361 MET cc_start: 0.7168 (mmp) cc_final: 0.6637 (mmp)
REVERT: A  628 MET cc_start: 0.8409 (mmm) cc_final: 0.8163 (mmp)
REVERT: A  683 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8310 (mt0)
  outliers start: 16
  outliers final: 9
  residues processed: 116
  average time/residue: 0.0644
  time to fit residues: 10.0194
Evaluate side-chains
  97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  683 GLN
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 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 = 0.4096 r_free = 0.4096 target = 0.170965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117304 restraints weight = 7523.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120971 restraints weight = 4143.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123011 restraints weight = 2988.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.124491 restraints weight = 2510.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.124970 restraints weight = 2281.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5165  Z= 0.211
  Angle     :  0.728  13.536   7006  Z= 0.371
  Chirality :  0.045   0.172    796
  Planarity :  0.005   0.051    856
  Dihedral  :  5.515  34.352    669
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.43 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.49 (0.34), residues: 611
  helix:  1.11 (0.26), residues: 381
  sheet: -2.21 (1.47), residues: 12
  loop : -2.96 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.022   0.002   TYR A 336 
 PHE   0.023   0.002   PHE A 733 
 TRP   0.037   0.003   TRP A 694 
 HIS   0.006   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 5165)
  covalent geometry    : angle       0.72842 ( 7006)
  hydrogen bonds       : bond        0.05638 (  309)
  hydrogen bonds       : angle       4.93687 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8823 (mm) cc_final: 0.8386 (tp)
REVERT: A  282 MET cc_start: 0.8552 (ptt) cc_final: 0.8310 (ptm)
REVERT: A  361 MET cc_start: 0.7191 (mmp) cc_final: 0.5960 (mmp)
  outliers start: 20
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0543
  time to fit residues: 7.7080
Evaluate side-chains
  95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.173579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.124411 restraints weight = 7412.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123787 restraints weight = 4565.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127085 restraints weight = 3219.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126988 restraints weight = 2621.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127203 restraints weight = 2386.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5165  Z= 0.159
  Angle     :  0.673  10.369   7006  Z= 0.339
  Chirality :  0.043   0.164    796
  Planarity :  0.004   0.049    856
  Dihedral  :  5.327  30.873    669
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.33 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.32 (0.35), residues: 611
  helix:  1.24 (0.27), residues: 381
  sheet: -1.84 (1.68), residues: 12
  loop : -2.89 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.021   0.001   TYR A 336 
 PHE   0.015   0.001   PHE A 712 
 TRP   0.035   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5165)
  covalent geometry    : angle       0.67335 ( 7006)
  hydrogen bonds       : bond        0.05320 (  309)
  hydrogen bonds       : angle       4.73684 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8834 (mm) cc_final: 0.8441 (tp)
REVERT: A  361 MET cc_start: 0.6937 (mmt) cc_final: 0.5732 (mmp)
  outliers start: 15
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0522
  time to fit residues: 7.3825
Evaluate side-chains
  97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 29 optimal weight:   40.0000
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.173944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.124964 restraints weight = 7485.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.124960 restraints weight = 4726.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127266 restraints weight = 3302.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.127528 restraints weight = 2573.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.127848 restraints weight = 2452.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5165  Z= 0.151
  Angle     :  0.669  12.811   7006  Z= 0.336
  Chirality :  0.044   0.199    796
  Planarity :  0.004   0.049    856
  Dihedral  :  5.269  31.104    669
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.78 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.29 (0.35), residues: 611
  helix:  1.20 (0.27), residues: 385
  sheet: -1.63 (1.54), residues: 12
  loop : -2.82 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.024   0.002   TYR A 336 
 PHE   0.012   0.001   PHE A 541 
 TRP   0.039   0.003   TRP A 407 
 HIS   0.004   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 5165)
  covalent geometry    : angle       0.66904 ( 7006)
  hydrogen bonds       : bond        0.05195 (  309)
  hydrogen bonds       : angle       4.68383 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8501 (t0) cc_final: 0.7751 (t0)
REVERT: A  349 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8816 (tpp80)
  outliers start: 22
  outliers final: 17
  residues processed: 101
  average time/residue: 0.0576
  time to fit residues: 8.0929
Evaluate side-chains
  103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 4 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.175074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.125970 restraints weight = 7526.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.126632 restraints weight = 4772.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128506 restraints weight = 3349.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.129151 restraints weight = 2543.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129329 restraints weight = 2451.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5165  Z= 0.145
  Angle     :  0.680  11.869   7006  Z= 0.337
  Chirality :  0.044   0.223    796
  Planarity :  0.004   0.048    856
  Dihedral  :  5.230  30.256    669
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.51 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.17 (0.35), residues: 611
  helix:  1.29 (0.27), residues: 382
  sheet: -2.21 (1.42), residues: 12
  loop : -2.69 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.022   0.001   TYR A 336 
 PHE   0.013   0.001   PHE A 712 
 TRP   0.044   0.003   TRP A 694 
 HIS   0.014   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5165)
  covalent geometry    : angle       0.68033 ( 7006)
  hydrogen bonds       : bond        0.05071 (  309)
  hydrogen bonds       : angle       4.61983 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8478 (t0) cc_final: 0.7761 (t0)
REVERT: A  260 PHE cc_start: 0.8455 (m-10) cc_final: 0.8010 (m-80)
REVERT: A  361 MET cc_start: 0.6260 (mmp) cc_final: 0.5568 (mmp)
REVERT: A  586 LEU cc_start: 0.8700 (tp) cc_final: 0.8427 (tp)
  outliers start: 22
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0631
  time to fit residues: 9.5765
Evaluate side-chains
  104 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.177054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.126275 restraints weight = 7592.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127665 restraints weight = 5116.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129701 restraints weight = 3445.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129722 restraints weight = 2674.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129945 restraints weight = 2596.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5165  Z= 0.139
  Angle     :  0.682  13.635   7006  Z= 0.339
  Chirality :  0.043   0.250    796
  Planarity :  0.004   0.044    856
  Dihedral  :  5.121  28.979    669
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 20.51 %
    Favored  : 75.32 %
  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: -0.02 (0.35), residues: 611
  helix:  1.43 (0.27), residues: 380
  sheet: -2.41 (1.37), residues: 12
  loop : -2.61 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.021   0.001   TYR A 336 
 PHE   0.017   0.001   PHE A 545 
 TRP   0.047   0.002   TRP A 694 
 HIS   0.017   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5165)
  covalent geometry    : angle       0.68198 ( 7006)
  hydrogen bonds       : bond        0.04899 (  309)
  hydrogen bonds       : angle       4.57038 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.7074 (m)
REVERT: A  197 ASN cc_start: 0.8419 (t0) cc_final: 0.7680 (t0)
REVERT: A  260 PHE cc_start: 0.8441 (m-10) cc_final: 0.7996 (m-80)
REVERT: A  361 MET cc_start: 0.5897 (mmp) cc_final: 0.5395 (mmp)
  outliers start: 23
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0637
  time to fit residues: 9.3765
Evaluate side-chains
  110 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0970
   chunk 47 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.177074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128372 restraints weight = 7466.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130191 restraints weight = 4526.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131869 restraints weight = 3075.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.132419 restraints weight = 2387.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.132493 restraints weight = 2421.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5165  Z= 0.142
  Angle     :  0.714  13.545   7006  Z= 0.350
  Chirality :  0.043   0.201    796
  Planarity :  0.004   0.043    856
  Dihedral  :  5.073  28.421    669
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.05 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.07 (0.35), residues: 611
  helix:  1.46 (0.27), residues: 381
  sheet: -2.37 (1.39), residues: 12
  loop : -2.52 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.024   0.001   TYR A 232 
 PHE   0.020   0.001   PHE A 545 
 TRP   0.040   0.002   TRP A 694 
 HIS   0.012   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5165)
  covalent geometry    : angle       0.71397 ( 7006)
  hydrogen bonds       : bond        0.04863 (  309)
  hydrogen bonds       : angle       4.58644 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6986 (m)
REVERT: A  197 ASN cc_start: 0.8411 (t0) cc_final: 0.7651 (t0)
REVERT: A  244 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7726 (tp)
REVERT: A  260 PHE cc_start: 0.8395 (m-10) cc_final: 0.7955 (m-80)
REVERT: A  338 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9113 (pttt)
REVERT: A  361 MET cc_start: 0.5858 (mmp) cc_final: 0.5411 (mmp)
  outliers start: 24
  outliers final: 19
  residues processed: 111
  average time/residue: 0.0683
  time to fit residues: 10.0749
Evaluate side-chains
  112 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0070
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.178836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.126524 restraints weight = 7457.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130582 restraints weight = 3996.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132817 restraints weight = 2816.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.134538 restraints weight = 2350.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.135124 restraints weight = 2115.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5165  Z= 0.141
  Angle     :  0.708  12.951   7006  Z= 0.353
  Chirality :  0.043   0.190    796
  Planarity :  0.004   0.042    856
  Dihedral  :  5.012  27.365    669
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.42 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.06 (0.35), residues: 611
  helix:  1.40 (0.27), residues: 384
  sheet: -2.31 (1.42), residues: 12
  loop : -2.47 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.027   0.001   TYR A 336 
 PHE   0.021   0.001   PHE A 545 
 TRP   0.052   0.002   TRP A 694 
 HIS   0.012   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5165)
  covalent geometry    : angle       0.70807 ( 7006)
  hydrogen bonds       : bond        0.04866 (  309)
  hydrogen bonds       : angle       4.63978 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8406 (t0) cc_final: 0.7660 (t0)
REVERT: A  244 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7662 (tp)
REVERT: A  260 PHE cc_start: 0.8381 (m-10) cc_final: 0.7954 (m-80)
REVERT: A  338 LYS cc_start: 0.9464 (mmtp) cc_final: 0.9090 (pttt)
REVERT: A  342 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8720 (mmmt)
REVERT: A  361 MET cc_start: 0.5674 (mmp) cc_final: 0.5234 (mmp)
REVERT: A  628 MET cc_start: 0.8244 (mmm) cc_final: 0.7913 (mmp)
  outliers start: 22
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0636
  time to fit residues: 9.2889
Evaluate side-chains
  112 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 HIS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0050
   chunk 21 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.179867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.132614 restraints weight = 7475.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.132382 restraints weight = 4846.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.133964 restraints weight = 3361.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.134879 restraints weight = 2724.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135098 restraints weight = 2538.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5165  Z= 0.145
  Angle     :  0.721  12.950   7006  Z= 0.358
  Chirality :  0.045   0.268    796
  Planarity :  0.004   0.039    856
  Dihedral  :  4.992  27.677    669
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 21.96 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.06 (0.35), residues: 611
  helix:  1.40 (0.27), residues: 384
  sheet: -2.30 (1.44), residues: 12
  loop : -2.46 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.026   0.002   TYR A 232 
 PHE   0.027   0.001   PHE A  52 
 TRP   0.050   0.002   TRP A 694 
 HIS   0.007   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5165)
  covalent geometry    : angle       0.72149 ( 7006)
  hydrogen bonds       : bond        0.04897 (  309)
  hydrogen bonds       : angle       4.62169 (  918)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7034 (m)
REVERT: A  197 ASN cc_start: 0.8433 (t0) cc_final: 0.7688 (t0)
REVERT: A  244 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7709 (tp)
REVERT: A  260 PHE cc_start: 0.8394 (m-10) cc_final: 0.7984 (m-80)
REVERT: A  338 LYS cc_start: 0.9458 (mmtp) cc_final: 0.9101 (pttt)
REVERT: A  342 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8715 (mmmt)
REVERT: A  361 MET cc_start: 0.5768 (mmp) cc_final: 0.5136 (mmp)
REVERT: A  628 MET cc_start: 0.8399 (mmm) cc_final: 0.8103 (mmp)
  outliers start: 21
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0657
  time to fit residues: 9.5896
Evaluate side-chains
  113 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  488 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.2980
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 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 = 0.4217 r_free = 0.4217 target = 0.180597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.133918 restraints weight = 7548.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133161 restraints weight = 5002.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135957 restraints weight = 3464.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.136257 restraints weight = 2527.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.136462 restraints weight = 2381.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5165  Z= 0.143
  Angle     :  0.727  14.773   7006  Z= 0.359
  Chirality :  0.045   0.250    796
  Planarity :  0.004   0.039    856
  Dihedral  :  4.971  26.846    669
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.14 %
    Favored  : 73.68 %
  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:  0.13 (0.35), residues: 611
  helix:  1.45 (0.27), residues: 383
  sheet: -2.30 (1.43), residues: 12
  loop : -2.41 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  63 
 TYR   0.025   0.001   TYR A 336 
 PHE   0.027   0.001   PHE A  52 
 TRP   0.047   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5165)
  covalent geometry    : angle       0.72716 ( 7006)
  hydrogen bonds       : bond        0.04832 (  309)
  hydrogen bonds       : angle       4.58834 (  918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1031.32 seconds
wall clock time: 18 minutes 28.94 seconds (1108.94 seconds total)