Starting phenix.real_space_refine
on Thu Mar  6 05:12:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw4_38730/03_2025/8xw4_38730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw4_38730/03_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_38730/03_2025/8xw4_38730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw4_38730/03_2025/8xw4_38730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw4_38730/03_2025/8xw4_38730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw4_38730/03_2025/8xw4_38730.cif"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.52, per 1000 atoms: 0.70
  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: 1.29
  Conformation dependent library (CDL) restraints added in 650.8 milliseconds
  

  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: 0.39
  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: 1.22

  Time building geometry restraints manager: 1.43 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.400
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.850
-------------------------------------------------------------------------------
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= 0.389
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (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
 TRP   0.068   0.004   TRP A 694 
 HIS   0.007   0.001   HIS A 656 
 PHE   0.025   0.002   PHE A 705 
 TYR   0.028   0.002   TYR A 297 
 ARG   0.003   0.000   ARG A  63 

*********************** 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  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8804 (mm) cc_final: 0.8210 (tp)
REVERT: A  260 PHE cc_start: 0.8500 (m-10) cc_final: 0.8070 (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: 0.8722 (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: 0.1442
  time to fit residues: 22.3881
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  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0970
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0970
   chunk 24 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.4116

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4144 r_free = 0.4144 target = 0.176538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127913 restraints weight = 7256.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128696 restraints weight = 4032.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130973 restraints weight = 2947.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5165  Z= 0.192
  Angle     :  0.690   8.759   7006  Z= 0.354
  Chirality :  0.044   0.176    796
  Planarity :  0.004   0.046    856
  Dihedral  :  5.548  31.080    669
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  9.98 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.35), residues: 611
  helix:  1.23 (0.27), residues: 379
  sheet: -3.04 (1.23), residues: 12
  loop : -2.95 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 694 
 HIS   0.005   0.001   HIS A 403 
 PHE   0.022   0.001   PHE A 712 
 TYR   0.019   0.002   TYR A 336 
 ARG   0.004   0.000   ARG A 293 

*********************** 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
  125 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8806 (mm) cc_final: 0.8431 (tp)
REVERT: A  260 PHE cc_start: 0.8462 (m-10) cc_final: 0.8070 (m-80)
REVERT: A  282 MET cc_start: 0.8465 (ptt) cc_final: 0.8265 (ptm)
REVERT: A  361 MET cc_start: 0.7194 (mmp) cc_final: 0.6683 (mmp)
REVERT: A  628 MET cc_start: 0.8379 (mmm) cc_final: 0.8148 (mmp)
REVERT: A  683 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8308 (mt0)
  outliers start: 16
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1454
  time to fit residues: 22.5841
Evaluate side-chains
  99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  207 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  435 LEU
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  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 48 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0570
   chunk 2 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 417 ASN
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4163 r_free = 0.4163 target = 0.177967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123132 restraints weight = 7579.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.127212 restraints weight = 4090.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129814 restraints weight = 2939.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5165  Z= 0.185
  Angle     :  0.662  12.224   7006  Z= 0.334
  Chirality :  0.042   0.173    796
  Planarity :  0.004   0.050    856
  Dihedral  :  5.217  30.810    669
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.97 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.35), residues: 611
  helix:  1.41 (0.27), residues: 375
  sheet: -2.11 (1.56), residues: 12
  loop : -2.89 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.017   0.001   PHE A 712 
 TYR   0.022   0.001   TYR A 336 
 ARG   0.003   0.000   ARG A 349 

*********************** 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
  118 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8807 (mm) cc_final: 0.8437 (tp)
REVERT: A  361 MET cc_start: 0.6763 (mmp) cc_final: 0.6169 (mmp)
REVERT: A  628 MET cc_start: 0.8495 (mmm) cc_final: 0.8295 (mmp)
REVERT: A  683 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8331 (mt0)
  outliers start: 18
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1415
  time to fit residues: 21.0541
Evaluate side-chains
  103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
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  207 LEU
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  636 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0470
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.9282

-------------------------------------------------------------------------------
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 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.177017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.121764 restraints weight = 7794.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.125797 restraints weight = 4223.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.128368 restraints weight = 3035.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2159

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= 0.211
  Angle     :  0.656  10.928   7006  Z= 0.330
  Chirality :  0.043   0.185    796
  Planarity :  0.004   0.049    856
  Dihedral  :  5.127  30.424    669
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.97 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.35), residues: 611
  helix:  1.47 (0.27), residues: 377
  sheet: -1.69 (1.62), residues: 12
  loop : -2.83 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.013   0.001   PHE A 541 
 TYR   0.021   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 349 

*********************** 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
  116 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8534 (t0) cc_final: 0.7817 (t0)
REVERT: A  244 ILE cc_start: 0.8788 (mm) cc_final: 0.8415 (tp)
REVERT: A  260 PHE cc_start: 0.8474 (m-10) cc_final: 0.8029 (m-80)
REVERT: A  349 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8776 (tpp80)
REVERT: A  361 MET cc_start: 0.6658 (mmt) cc_final: 0.5887 (mmp)
REVERT: A  628 MET cc_start: 0.8557 (mmm) cc_final: 0.8339 (mmp)
REVERT: A  683 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8331 (mt0)
  outliers start: 20
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1908
  time to fit residues: 27.4518
Evaluate side-chains
  108 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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  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  488 SER
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  683 GLN
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 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   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 150 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4168 r_free = 0.4168 target = 0.177654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.125362 restraints weight = 7389.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129301 restraints weight = 3924.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.131881 restraints weight = 2778.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   5165  Z= 0.205
  Angle     :  0.650   9.932   7006  Z= 0.327
  Chirality :  0.042   0.181    796
  Planarity :  0.004   0.047    856
  Dihedral  :  5.043  29.292    669
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 17.42 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.35), residues: 611
  helix:  1.42 (0.26), residues: 383
  sheet: -1.80 (1.53), residues: 12
  loop : -2.67 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 694 
 HIS   0.022   0.002   HIS A 150 
 PHE   0.011   0.001   PHE A 541 
 TYR   0.022   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 349 

*********************** 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
  125 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8486 (t0) cc_final: 0.7800 (t0)
REVERT: A  244 ILE cc_start: 0.8793 (mm) cc_final: 0.8508 (tp)
REVERT: A  260 PHE cc_start: 0.8467 (m-10) cc_final: 0.8023 (m-80)
REVERT: A  298 PHE cc_start: 0.8908 (m-10) cc_final: 0.8705 (m-10)
REVERT: A  338 LYS cc_start: 0.9428 (mmtp) cc_final: 0.9065 (pttt)
REVERT: A  349 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8601 (tpp80)
REVERT: A  361 MET cc_start: 0.6468 (mmt) cc_final: 0.5696 (mmp)
REVERT: A  628 MET cc_start: 0.8516 (mmm) cc_final: 0.8142 (mmp)
REVERT: A  683 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8326 (mt0)
  outliers start: 24
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1588
  time to fit residues: 23.9992
Evaluate side-chains
  111 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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  194 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  449 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4214 r_free = 0.4214 target = 0.180595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133136 restraints weight = 7502.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.134162 restraints weight = 4448.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136683 restraints weight = 2940.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5165  Z= 0.180
  Angle     :  0.663  12.540   7006  Z= 0.330
  Chirality :  0.043   0.220    796
  Planarity :  0.004   0.043    856
  Dihedral  :  4.998  28.500    669
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.60 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.35), residues: 611
  helix:  1.53 (0.27), residues: 382
  sheet: -1.61 (1.54), residues: 12
  loop : -2.56 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP A 694 
 HIS   0.004   0.001   HIS A 656 
 PHE   0.017   0.001   PHE A 545 
 TYR   0.025   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A  63 

*********************** 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
  119 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8449 (t0) cc_final: 0.7772 (t0)
REVERT: A  244 ILE cc_start: 0.8631 (mm) cc_final: 0.8367 (tp)
REVERT: A  260 PHE cc_start: 0.8412 (m-10) cc_final: 0.8010 (m-80)
REVERT: A  338 LYS cc_start: 0.9439 (mmtp) cc_final: 0.9084 (pttt)
REVERT: A  361 MET cc_start: 0.6525 (mmt) cc_final: 0.5903 (mmp)
REVERT: A  683 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8326 (mt0)
  outliers start: 18
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1475
  time to fit residues: 21.4375
Evaluate side-chains
  110 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
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  194 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  417 ASN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  640 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0020
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4176 r_free = 0.4176 target = 0.178328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126559 restraints weight = 7452.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130478 restraints weight = 4130.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132860 restraints weight = 2959.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2885

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= 0.186
  Angle     :  0.651   9.557   7006  Z= 0.332
  Chirality :  0.042   0.183    796
  Planarity :  0.004   0.042    856
  Dihedral  :  4.920  28.023    669
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.42 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.35), residues: 611
  helix:  1.66 (0.27), residues: 382
  sheet: -1.62 (1.51), residues: 12
  loop : -2.52 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.020   0.001   PHE A 545 
 TYR   0.024   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 349 

*********************** 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
  121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8394 (t0) cc_final: 0.7648 (t0)
REVERT: A  244 ILE cc_start: 0.8700 (mm) cc_final: 0.8379 (tp)
REVERT: A  260 PHE cc_start: 0.8429 (m-10) cc_final: 0.8018 (m-80)
REVERT: A  338 LYS cc_start: 0.9452 (mmtp) cc_final: 0.9103 (pttt)
REVERT: A  361 MET cc_start: 0.6101 (mmt) cc_final: 0.5548 (mmp)
REVERT: A  683 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8348 (mt0)
  outliers start: 24
  outliers final: 21
  residues processed: 109
  average time/residue: 0.2082
  time to fit residues: 30.9982
Evaluate side-chains
  115 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
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  207 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 VAL
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  636 THR
Chi-restraints excluded: chain A residue  640 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4173 r_free = 0.4173 target = 0.177964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.126006 restraints weight = 7528.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129764 restraints weight = 4186.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132181 restraints weight = 3010.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2939

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= 0.199
  Angle     :  0.667  10.698   7006  Z= 0.339
  Chirality :  0.044   0.247    796
  Planarity :  0.004   0.039    856
  Dihedral  :  4.900  28.252    669
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.35), residues: 611
  helix:  1.57 (0.27), residues: 383
  sheet: -1.60 (1.50), residues: 12
  loop : -2.51 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.023   0.001   PHE A 545 
 TYR   0.023   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 349 

*********************** 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
  117 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8405 (t0) cc_final: 0.7623 (t0)
REVERT: A  244 ILE cc_start: 0.8691 (mm) cc_final: 0.8371 (tp)
REVERT: A  260 PHE cc_start: 0.8449 (m-10) cc_final: 0.8038 (m-80)
REVERT: A  338 LYS cc_start: 0.9468 (mmtp) cc_final: 0.9144 (pttt)
REVERT: A  361 MET cc_start: 0.6146 (mmt) cc_final: 0.5635 (mmp)
REVERT: A  683 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8351 (mt0)
  outliers start: 22
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1890
  time to fit residues: 26.9389
Evaluate side-chains
  116 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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  217 LEU
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  640 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0010
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4233 r_free = 0.4233 target = 0.182216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.135690 restraints weight = 7430.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137632 restraints weight = 4467.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.139381 restraints weight = 3006.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5165  Z= 0.192
  Angle     :  0.680   9.348   7006  Z= 0.343
  Chirality :  0.044   0.234    796
  Planarity :  0.004   0.036    856
  Dihedral  :  4.807  25.860    669
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.36), residues: 611
  helix:  1.65 (0.27), residues: 383
  sheet: -1.65 (1.50), residues: 12
  loop : -2.44 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.026   0.001   PHE A 545 
 TYR   0.024   0.001   TYR A 232 
 ARG   0.002   0.000   ARG A  63 

*********************** 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
  115 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8324 (t0) cc_final: 0.7609 (t0)
REVERT: A  260 PHE cc_start: 0.8363 (m-10) cc_final: 0.8005 (m-80)
REVERT: A  338 LYS cc_start: 0.9443 (mmtp) cc_final: 0.9150 (pttt)
REVERT: A  361 MET cc_start: 0.6401 (mmt) cc_final: 0.5764 (mmp)
REVERT: A  377 LYS cc_start: 0.8930 (mttp) cc_final: 0.8648 (mttp)
REVERT: A  683 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8308 (mt0)
  outliers start: 17
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1492
  time to fit residues: 21.0116
Evaluate side-chains
  105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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  194 THR
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
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  683 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0060
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 5 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0970
   chunk 26 optimal weight:    9.9990
   chunk 39 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4394

-------------------------------------------------------------------------------
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 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4209 r_free = 0.4209 target = 0.181453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129864 restraints weight = 7475.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133879 restraints weight = 4045.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.136454 restraints weight = 2869.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5165  Z= 0.195
  Angle     :  0.704  11.160   7006  Z= 0.352
  Chirality :  0.043   0.242    796
  Planarity :  0.004   0.031    856
  Dihedral  :  4.834  24.256    669
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.69 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.35), residues: 611
  helix:  1.63 (0.27), residues: 385
  sheet: -2.37 (1.31), residues: 12
  loop : -2.27 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.028   0.001   PHE A 545 
 TYR   0.025   0.001   TYR A 336 
 ARG   0.001   0.000   ARG A 587 

********************** 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
  113 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8319 (t0) cc_final: 0.7561 (t0)
REVERT: A  244 ILE cc_start: 0.8436 (tp) cc_final: 0.8037 (tp)
REVERT: A  260 PHE cc_start: 0.8424 (m-10) cc_final: 0.7979 (m-80)
REVERT: A  338 LYS cc_start: 0.9471 (mmtp) cc_final: 0.9148 (pttt)
REVERT: A  361 MET cc_start: 0.5753 (mmt) cc_final: 0.5045 (mmp)
REVERT: A  377 LYS cc_start: 0.8961 (mttp) cc_final: 0.8690 (mttp)
REVERT: A  683 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8349 (mt0)
  outliers start: 16
  outliers final: 12
  residues processed: 103
  average time/residue: 0.2467
  time to fit residues: 34.2948
Evaluate side-chains
  105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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  194 THR
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  364 VAL
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:   30.0000
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0030
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 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 = 0.4241 r_free = 0.4241 target = 0.182916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137047 restraints weight = 7527.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.136235 restraints weight = 5029.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137386 restraints weight = 3728.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5165  Z= 0.201
  Angle     :  0.728  13.809   7006  Z= 0.359
  Chirality :  0.044   0.232    796
  Planarity :  0.004   0.027    856
  Dihedral  :  4.789  24.944    669
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.35), residues: 611
  helix:  1.65 (0.27), residues: 386
  sheet: -2.36 (1.27), residues: 12
  loop : -2.25 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.028   0.001   PHE A 545 
 TYR   0.026   0.001   TYR A 232 
 ARG   0.007   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2465.08 seconds
wall clock time: 46 minutes 30.07 seconds (2790.07 seconds total)