Starting phenix.real_space_refine
on Tue Feb 11 09:12:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw4_38730/02_2025/8xw4_38730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw4_38730/02_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_38730/02_2025/8xw4_38730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw4_38730/02_2025/8xw4_38730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw4_38730/02_2025/8xw4_38730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw4_38730/02_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-5592/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: 3.40, per 1000 atoms: 0.68
  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 609.6 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: 0.40
  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: 1.24

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.21 -     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:             0.940
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.150
  Find NCS groups from input model:        0.050
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
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  : 0.530 
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: 0.1617
  time to fit residues: 24.9919
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  : 0.536 
-------------------------------------------------------------------------------
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 = 0.127912 restraints weight = 7256.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128699 restraints weight = 4032.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131035 restraints weight = 2937.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
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  : 0.564 
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: 0.8264 (ptm)
REVERT: A  361 MET cc_start: 0.7195 (mmp) cc_final: 0.6683 (mmp)
REVERT: A  628 MET cc_start: 0.8381 (mmm) cc_final: 0.8149 (mmp)
REVERT: A  683 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8309 (mt0)
  outliers start: 16
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1529
  time to fit residues: 23.7262
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  : 0.572 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 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 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 = 0.4137 r_free = 0.4137 target = 0.175409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.124978 restraints weight = 7607.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.123949 restraints weight = 4657.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.125639 restraints weight = 3720.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1835

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= 0.223
  Angle     :  0.680  12.540   7006  Z= 0.344
  Chirality :  0.043   0.171    796
  Planarity :  0.004   0.051    856
  Dihedral  :  5.321  32.348    669
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.16 %
    Favored  : 82.40 %
  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: -0.31 (0.35), residues: 611
  helix:  1.25 (0.27), residues: 381
  sheet: -2.22 (1.53), residues: 12
  loop : -2.86 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.018   0.001   PHE A 712 
 TYR   0.022   0.002   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
  116 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ILE cc_start: 0.8836 (mm) cc_final: 0.8451 (tp)
REVERT: A  282 MET cc_start: 0.8447 (ptt) cc_final: 0.8203 (ptm)
REVERT: A  361 MET cc_start: 0.7051 (mmp) cc_final: 0.6249 (mmp)
REVERT: A  628 MET cc_start: 0.8314 (mmm) cc_final: 0.8018 (mmp)
REVERT: A  683 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8346 (mt0)
  outliers start: 19
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1240
  time to fit residues: 18.3740
Evaluate side-chains
  100 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0970
   chunk 17 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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
** 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 = 0.4166 r_free = 0.4166 target = 0.178113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130185 restraints weight = 7780.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130009 restraints weight = 5033.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131390 restraints weight = 4621.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5165  Z= 0.211
  Angle     :  0.672  12.213   7006  Z= 0.334
  Chirality :  0.043   0.170    796
  Planarity :  0.004   0.049    856
  Dihedral  :  5.146  29.205    669
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.42 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.35), residues: 611
  helix:  1.35 (0.27), residues: 382
  sheet: -1.39 (1.77), residues: 12
  loop : -2.73 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A 656 
 PHE   0.017   0.001   PHE A  52 
 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
  114 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A  197 ASN cc_start: 0.8510 (t0) cc_final: 0.7825 (t0)
REVERT: A  244 ILE cc_start: 0.8735 (mm) cc_final: 0.8510 (tp)
REVERT: A  260 PHE cc_start: 0.8383 (m-10) cc_final: 0.7976 (m-80)
REVERT: A  338 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8968 (pttt)
REVERT: A  349 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8794 (tpp80)
REVERT: A  361 MET cc_start: 0.6946 (mmt) cc_final: 0.6117 (mmp)
REVERT: A  628 MET cc_start: 0.8325 (mmm) cc_final: 0.8100 (mmp)
REVERT: A  683 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8322 (mt0)
  outliers start: 18
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1430
  time to fit residues: 20.4313
Evaluate side-chains
  103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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  488 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.177209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.124961 restraints weight = 7388.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129021 restraints weight = 3895.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131535 restraints weight = 2738.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2429

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= 0.190
  Angle     :  0.655  12.963   7006  Z= 0.327
  Chirality :  0.042   0.189    796
  Planarity :  0.004   0.047    856
  Dihedral  :  5.073  29.131    669
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.97 %
    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: -0.02 (0.35), residues: 611
  helix:  1.39 (0.27), residues: 385
  sheet: -1.50 (1.57), residues: 12
  loop : -2.70 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 407 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.018   0.001   PHE A  52 
 TYR   0.024   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 293 

*********************** 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
  123 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8498 (t0) cc_final: 0.7812 (t0)
REVERT: A  244 ILE cc_start: 0.8714 (mm) cc_final: 0.8331 (tp)
REVERT: A  260 PHE cc_start: 0.8480 (m-10) cc_final: 0.8036 (m-80)
REVERT: A  338 LYS cc_start: 0.9409 (mmtp) cc_final: 0.9024 (pttt)
REVERT: A  349 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8595 (tpp80)
REVERT: A  361 MET cc_start: 0.6601 (mmt) cc_final: 0.5749 (mmp)
REVERT: A  628 MET cc_start: 0.8519 (mmm) cc_final: 0.8141 (mmp)
REVERT: A  683 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8350 (mt0)
  outliers start: 21
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1591
  time to fit residues: 24.5064
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  : 0.534 
-------------------------------------------------------------------------------
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  292 GLU
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  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  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:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0050
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0000
   chunk 0 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.3798

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.179101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.126702 restraints weight = 7524.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130948 restraints weight = 3913.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.133614 restraints weight = 2724.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5165  Z= 0.177
  Angle     :  0.660  11.338   7006  Z= 0.330
  Chirality :  0.043   0.224    796
  Planarity :  0.004   0.042    856
  Dihedral  :  5.013  28.354    669
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.42 %
    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:  0.12 (0.35), residues: 611
  helix:  1.50 (0.27), residues: 384
  sheet: -1.64 (1.53), residues: 12
  loop : -2.59 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 694 
 HIS   0.018   0.001   HIS A 150 
 PHE   0.020   0.001   PHE A  52 
 TYR   0.023   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 293 

*********************** 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
  122 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8432 (t0) cc_final: 0.7723 (t0)
REVERT: A  244 ILE cc_start: 0.8734 (mm) cc_final: 0.8398 (tp)
REVERT: A  260 PHE cc_start: 0.8459 (m-10) cc_final: 0.8015 (m-80)
REVERT: A  338 LYS cc_start: 0.9447 (mmtp) cc_final: 0.9091 (pttt)
REVERT: A  361 MET cc_start: 0.6343 (mmt) cc_final: 0.5722 (mmp)
REVERT: A  683 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8349 (mt0)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1531
  time to fit residues: 22.6893
Evaluate side-chains
  110 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  292 GLU
Chi-restraints excluded: chain A residue  417 ASN
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 367 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.175622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127087 restraints weight = 7489.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.126405 restraints weight = 5222.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129635 restraints weight = 3623.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5165  Z= 0.243
  Angle     :  0.692  14.503   7006  Z= 0.348
  Chirality :  0.044   0.228    796
  Planarity :  0.004   0.041    856
  Dihedral  :  5.042  30.471    669
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.69 %
    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 (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:  0.08 (0.35), residues: 611
  helix:  1.49 (0.27), residues: 380
  sheet: -1.69 (1.50), residues: 12
  loop : -2.56 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 694 
 HIS   0.011   0.001   HIS A 150 
 PHE   0.021   0.001   PHE A 545 
 TYR   0.022   0.002   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
  116 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8453 (t0) cc_final: 0.7690 (t0)
REVERT: A  244 ILE cc_start: 0.8768 (mm) cc_final: 0.8405 (tp)
REVERT: A  260 PHE cc_start: 0.8451 (m-10) cc_final: 0.8021 (m-80)
REVERT: A  361 MET cc_start: 0.6551 (mmt) cc_final: 0.5801 (mmp)
REVERT: A  683 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (mt0)
  outliers start: 21
  outliers final: 18
  residues processed: 104
  average time/residue: 0.1460
  time to fit residues: 20.4482
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  : 0.558 
-------------------------------------------------------------------------------
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0980
   chunk 18 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.179998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.131747 restraints weight = 7492.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132403 restraints weight = 4865.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.134533 restraints weight = 3245.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2898

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= 0.194
  Angle     :  0.693  13.564   7006  Z= 0.343
  Chirality :  0.043   0.199    796
  Planarity :  0.004   0.039    856
  Dihedral  :  4.986  27.915    669
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 21.05 %
    Favored  : 75.14 %
  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:  1.54 (0.27), residues: 381
  sheet: -1.67 (1.52), residues: 12
  loop : -2.55 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A 694 
 HIS   0.014   0.001   HIS A 150 
 PHE   0.024   0.001   PHE A 428 
 TYR   0.022   0.001   TYR A 336 
 ARG   0.003   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: 21
    poor density    : 96
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8427 (t0) cc_final: 0.7677 (t0)
REVERT: A  244 ILE cc_start: 0.8720 (mm) cc_final: 0.8444 (tp)
REVERT: A  260 PHE cc_start: 0.8417 (m-10) cc_final: 0.8006 (m-80)
REVERT: A  338 LYS cc_start: 0.9447 (mmtp) cc_final: 0.9107 (pttt)
REVERT: A  361 MET cc_start: 0.6520 (mmt) cc_final: 0.5761 (mmp)
REVERT: A  683 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8297 (mt0)
  outliers start: 21
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1506
  time to fit residues: 21.3109
Evaluate side-chains
  109 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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  269 VAL
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  417 ASN
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  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:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4174 r_free = 0.4174 target = 0.178290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129009 restraints weight = 7495.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130073 restraints weight = 4887.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132188 restraints weight = 3221.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3002

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= 0.201
  Angle     :  0.691  13.276   7006  Z= 0.345
  Chirality :  0.043   0.192    796
  Planarity :  0.004   0.039    856
  Dihedral  :  4.931  27.799    669
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.50 %
    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 (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:  0.08 (0.35), residues: 611
  helix:  1.43 (0.27), residues: 383
  sheet: -1.68 (1.51), residues: 12
  loop : -2.52 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 694 
 HIS   0.012   0.001   HIS A 150 
 PHE   0.025   0.001   PHE A  52 
 TYR   0.025   0.001   TYR A 232 
 ARG   0.003   0.000   ARG A 349 

*********************** 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: 18
    poor density    : 97
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8416 (t0) cc_final: 0.7644 (t0)
REVERT: A  244 ILE cc_start: 0.8734 (mm) cc_final: 0.8437 (tp)
REVERT: A  260 PHE cc_start: 0.8399 (m-10) cc_final: 0.7986 (m-80)
REVERT: A  361 MET cc_start: 0.6455 (mmt) cc_final: 0.5787 (mmp)
REVERT: A  683 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8353 (mt0)
  outliers start: 18
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1468
  time to fit residues: 20.7686
Evaluate side-chains
  110 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 52 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0050
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0970
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.3992

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.179748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.131775 restraints weight = 7452.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132134 restraints weight = 5044.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.134527 restraints weight = 3430.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5165  Z= 0.195
  Angle     :  0.695  12.798   7006  Z= 0.347
  Chirality :  0.043   0.255    796
  Planarity :  0.004   0.037    856
  Dihedral  :  4.883  25.968    669
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.05 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.14 (0.35), residues: 611
  helix:  1.46 (0.27), residues: 384
  sheet: -1.70 (1.52), residues: 12
  loop : -2.46 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 694 
 HIS   0.013   0.001   HIS A 150 
 PHE   0.026   0.001   PHE A 545 
 TYR   0.022   0.001   TYR A 336 
 ARG   0.002   0.000   ARG A 349 

********************** 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: 17
    poor density    : 98
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ASN cc_start: 0.8335 (t0) cc_final: 0.7602 (t0)
REVERT: A  244 ILE cc_start: 0.8713 (mm) cc_final: 0.8484 (tp)
REVERT: A  260 PHE cc_start: 0.8376 (m-10) cc_final: 0.7985 (m-80)
REVERT: A  338 LYS cc_start: 0.9462 (mmtp) cc_final: 0.9140 (pttt)
REVERT: A  361 MET cc_start: 0.6437 (mmt) cc_final: 0.5829 (mmp)
REVERT: A  377 LYS cc_start: 0.8945 (mttp) cc_final: 0.8650 (mttp)
REVERT: A  683 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8330 (mt0)
  outliers start: 17
  outliers final: 15
  residues processed: 104
  average time/residue: 0.1511
  time to fit residues: 20.7955
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  : 0.606 
-------------------------------------------------------------------------------
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  417 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   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 = 0.4185 r_free = 0.4185 target = 0.179410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130443 restraints weight = 7559.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131073 restraints weight = 5198.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.133567 restraints weight = 3445.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5165  Z= 0.212
  Angle     :  0.721  13.579   7006  Z= 0.357
  Chirality :  0.044   0.259    796
  Planarity :  0.004   0.037    856
  Dihedral  :  4.901  25.884    669
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.41 %
    Favored  : 73.32 %
  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:  0.20 (0.35), residues: 611
  helix:  1.47 (0.27), residues: 385
  sheet: -1.64 (1.51), residues: 12
  loop : -2.38 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A 694 
 HIS   0.013   0.001   HIS A 150 
 PHE   0.027   0.001   PHE A 545 
 TYR   0.025   0.001   TYR A 232 
 ARG   0.002   0.000   ARG A 587 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1909.02 seconds
wall clock time: 35 minutes 35.10 seconds (2135.10 seconds total)