Starting phenix.real_space_refine
on Mon Jan 13 20:07:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx1_37897/01_2025/8wx1_37897.cif"
  }
  resolution = 3.64
  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=   0.002 sd=   0.038
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      23      5.16       5
     C    2593      2.51       5
     N     640      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3926
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3926
          Classifications: {'peptide': 500}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 474}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.80, per 1000 atoms: 0.71
  Number of scatterers: 3926
  At special positions: 0
  Unit cell: (79.68, 74.1467, 69.72, 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      23     16.00
     O     670      8.00
     N     640      7.00
     C    2593      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 523 " - pdb=" SG  CYS A 533 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 396.9 milliseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  926

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 1 sheets defined
      79.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 61
      removed outlier: 4.118A  pdb=" N   ASN A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   VAL A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 97
      Proline residue:  A  88  - end of helix
      removed outlier: 4.076A  pdb=" N   TYR A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 123
    Processing helix  chain 'A' and resid 123 through 131
      removed outlier: 3.586A  pdb=" N   CYS A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 187
    Processing helix  chain 'A' and resid 191 through 224
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 3.884A  pdb=" N   GLY A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 300 through 341
      Proline residue:  A 316  - end of helix
      Proline residue:  A 323  - end of helix
      removed outlier: 3.641A  pdb=" N   HIS A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 399
      removed outlier: 3.677A  pdb=" N   LEU A 383 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 384 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      Proline residue:  A 385  - end of helix
      Proline residue:  A 393  - end of helix
    Processing helix  chain 'A' and resid 403 through 435
      removed outlier: 3.597A  pdb=" N   ALA A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 457 through 483
      removed outlier: 4.556A  pdb=" N   GLN A 461 " --> pdb=" O   TRP A 457 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 488 through 515
    Processing helix  chain 'A' and resid 535 through 566
    Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 443
      removed outlier: 3.961A  pdb=" N   ILE A 443 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 446 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    939 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: 1.09

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1194
        1.34 -     1.46: 919
        1.46 -     1.58: 1879
        1.58 -     1.70: 0
        1.70 -     1.81: 37
  Bond restraints: 4029
  Sorted by residual:
  bond pdb=" C   SER A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.331  1.362 -0.031 1.27e-02 6.20e+03 5.85e+00
  bond pdb=" C   VAL A 322 "
       pdb=" N   PRO A 323 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.77e+00
  bond pdb=" C   ILE A 474 "
       pdb=" N   PRO A 475 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.19e+00
  bond pdb=" C   ALA A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.20e-02 6.94e+03 3.12e+00
  bond pdb=" C   LEU A 315 "
       pdb=" N   PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.87e+00
  ... (remaining 4024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 5103
        1.29 -     2.59: 298
        2.59 -     3.88: 59
        3.88 -     5.17: 20
        5.17 -     6.47: 7
  Bond angle restraints: 5487
  Sorted by residual:
  angle pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
        pdb=" C   VAL A 187 "
      ideal   model   delta    sigma   weight residual
     111.91  108.05    3.86 8.90e-01 1.26e+00 1.88e+01
  angle pdb=" C   GLN A 458 "
        pdb=" N   ILE A 459 "
        pdb=" CA  ILE A 459 "
      ideal   model   delta    sigma   weight residual
     120.33  123.30   -2.97 8.00e-01 1.56e+00 1.38e+01
  angle pdb=" C   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     113.70  110.40    3.30 9.50e-01 1.11e+00 1.21e+01
  angle pdb=" C   TRP A 152 "
        pdb=" N   SER A 153 "
        pdb=" CA  SER A 153 "
      ideal   model   delta    sigma   weight residual
     122.74  127.50   -4.76 1.44e+00 4.82e-01 1.09e+01
  angle pdb=" CA  ARG A 366 "
        pdb=" C   ARG A 366 "
        pdb=" N   ILE A 367 "
      ideal   model   delta    sigma   weight residual
     114.17  118.88   -4.71 1.45e+00 4.76e-01 1.05e+01
  ... (remaining 5482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2100
       17.16 -    34.33: 207
       34.33 -    51.49: 31
       51.49 -    68.66: 6
       68.66 -    85.82: 4
  Dihedral angle restraints: 2348
    sinusoidal: 906
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" CA  MET A 188 "
           pdb=" C   MET A 188 "
           pdb=" N   ASP A 189 "
           pdb=" CA  ASP A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.74  -32.26     0      5.00e+00 4.00e-02 4.16e+01
  dihedral pdb=" CA  CYS A 273 "
           pdb=" C   CYS A 273 "
           pdb=" N   PRO A 274 "
           pdb=" CA  PRO A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.53   16.47     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASN A 346 "
           pdb=" CB  ASN A 346 "
           pdb=" CG  ASN A 346 "
           pdb=" OD1 ASN A 346 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -174.37  -65.63     2      2.00e+01 2.50e-03 9.96e+00
  ... (remaining 2345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 436
       0.027 -    0.054: 100
       0.054 -    0.081: 68
       0.081 -    0.109: 20
       0.109 -    0.136: 5
  Chirality restraints: 629
  Sorted by residual:
  chirality pdb=" CA  ILE A 224 "
            pdb=" N   ILE A 224 "
            pdb=" C   ILE A 224 "
            pdb=" CB  ILE A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 344 "
            pdb=" N   ILE A 344 "
            pdb=" C   ILE A 344 "
            pdb=" CB  ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  PRO A 368 "
            pdb=" N   PRO A 368 "
            pdb=" C   PRO A 368 "
            pdb=" CB  PRO A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 626 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  26 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A  27 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 214 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" C   LEU A 214 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 214 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 215 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 439 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO A 440 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1147
        2.82 -     3.34: 4189
        3.34 -     3.86: 6800
        3.86 -     4.38: 7128
        4.38 -     4.90: 12352
  Nonbonded interactions: 31616
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  29 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER A 259 "
            pdb=" OG  SER A 259 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASP A 526 "
            pdb=" ND2 ASN A 529 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   PRO A 402 "
            pdb=" NZ  LYS A 407 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   MET A 188 "
            pdb=" N   LEU A 190 "
     model   vdw
     2.400 3.120
  ... (remaining 31611 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.130
  Find NCS groups from input model:        0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
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      :  0.003   0.031   4029  Z= 0.171
  Angle     :  0.737   6.466   5487  Z= 0.464
  Chirality :  0.035   0.136    629
  Planarity :  0.004   0.041    680
  Dihedral  : 13.802  85.821   1416
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.67 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.07 (0.37), residues: 492
  helix:  0.75 (0.24), residues: 386
  sheet:  None (None), residues: 0
  loop : -2.47 (0.69), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.010   0.001   PHE A 479 
 TYR   0.012   0.001   TYR A 324 
 ARG   0.003   0.000   ARG A 196 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: A  474 ILE cc_start: 0.8674 (mm) cc_final: 0.8357 (mm)
REVERT: A  552 LEU cc_start: 0.8554 (tp) cc_final: 0.8319 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1505
  time to fit residues: 29.0515
Evaluate side-chains
  109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0270
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0050
   overall best weight:    0.5652

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 565 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.180347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153231 restraints weight = 5264.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.157522 restraints weight = 2837.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.160133 restraints weight = 1933.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4029  Z= 0.196
  Angle     :  0.668  10.130   5487  Z= 0.327
  Chirality :  0.039   0.178    629
  Planarity :  0.005   0.038    680
  Dihedral  :  4.336  26.714    540
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.08 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.42 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.40), residues: 492
  helix:  1.78 (0.26), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.75 (0.71), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.024   0.001   PHE A 496 
 TYR   0.021   0.002   TYR A 481 
 ARG   0.004   0.001   ARG A 349 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.7573 (p0) cc_final: 0.7370 (p0)
REVERT: A  188 MET cc_start: 0.7790 (tpp) cc_final: 0.6970 (ttt)
REVERT: A  335 TYR cc_start: 0.8565 (m-10) cc_final: 0.8242 (m-10)
REVERT: A  552 LEU cc_start: 0.8630 (tp) cc_final: 0.8334 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 116
  average time/residue: 0.1258
  time to fit residues: 19.3026
Evaluate side-chains
  111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   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 330 GLN
A 332 GLN
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 489 GLN ** 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 = 0.3980 r_free = 0.3980 target = 0.174087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147048 restraints weight = 5382.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.151246 restraints weight = 2913.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154034 restraints weight = 1987.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4029  Z= 0.219
  Angle     :  0.638   9.850   5487  Z= 0.317
  Chirality :  0.041   0.198    629
  Planarity :  0.005   0.039    680
  Dihedral  :  4.255  24.522    540
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.28 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.77 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.40), residues: 492
  helix:  1.94 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -1.47 (0.76), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  30 
 HIS   0.001   0.001   HIS A 341 
 PHE   0.021   0.002   PHE A 496 
 TYR   0.012   0.001   TYR A 324 
 ARG   0.003   0.000   ARG A 192 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8674 (t0) cc_final: 0.8444 (t0)
REVERT: A  328 TYR cc_start: 0.8970 (t80) cc_final: 0.8637 (t80)
REVERT: A  335 TYR cc_start: 0.8682 (m-10) cc_final: 0.8208 (m-10)
REVERT: A  449 TYR cc_start: 0.7233 (m-80) cc_final: 0.7012 (m-80)
REVERT: A  552 LEU cc_start: 0.8582 (tp) cc_final: 0.8340 (tt)
REVERT: A  561 GLU cc_start: 0.8437 (tp30) cc_final: 0.8164 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1185
  time to fit residues: 17.6361
Evaluate side-chains
  108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0370
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 489 GLN ** 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 = 0.3980 r_free = 0.3980 target = 0.174307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146482 restraints weight = 5444.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150717 restraints weight = 2977.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153588 restraints weight = 2044.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4029  Z= 0.190
  Angle     :  0.621   8.364   5487  Z= 0.310
  Chirality :  0.040   0.173    629
  Planarity :  0.005   0.039    680
  Dihedral  :  4.281  23.824    540
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.89 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.25 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.41), residues: 492
  helix:  2.11 (0.26), residues: 384
  sheet: -2.61 (1.29), residues: 10
  loop : -1.01 (0.83), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.023   0.001   PHE A 527 
 TYR   0.016   0.001   TYR A 560 
 ARG   0.006   0.000   ARG A  31 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8569 (tp) cc_final: 0.8316 (tp)
REVERT: A  185 ASP cc_start: 0.8766 (t0) cc_final: 0.8498 (t0)
REVERT: A  328 TYR cc_start: 0.8911 (t80) cc_final: 0.8438 (t80)
REVERT: A  335 TYR cc_start: 0.8628 (m-10) cc_final: 0.8215 (m-10)
REVERT: A  552 LEU cc_start: 0.8623 (tp) cc_final: 0.8400 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1148
  time to fit residues: 16.5030
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
** A 489 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.169835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.141981 restraints weight = 5615.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146142 restraints weight = 3052.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148907 restraints weight = 2095.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4029  Z= 0.223
  Angle     :  0.634   7.676   5487  Z= 0.319
  Chirality :  0.042   0.158    629
  Planarity :  0.005   0.043    680
  Dihedral  :  4.239  21.946    540
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 24.40 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.41), residues: 492
  helix:  2.14 (0.26), residues: 382
  sheet: -1.98 (1.63), residues: 10
  loop : -0.83 (0.82), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.030   0.002   PHE A 527 
 TYR   0.012   0.001   TYR A 324 
 ARG   0.003   0.001   ARG A 127 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8628 (tp) cc_final: 0.8377 (tp)
REVERT: A  125 ASP cc_start: 0.7930 (m-30) cc_final: 0.7563 (t0)
REVERT: A  185 ASP cc_start: 0.8701 (t0) cc_final: 0.8368 (t0)
REVERT: A  328 TYR cc_start: 0.8983 (t80) cc_final: 0.8561 (t80)
REVERT: A  335 TYR cc_start: 0.8648 (m-10) cc_final: 0.8320 (m-10)
REVERT: A  369 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: A  527 PHE cc_start: 0.4984 (p90) cc_final: 0.4706 (p90)
REVERT: A  561 GLU cc_start: 0.8399 (tp30) cc_final: 0.8060 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1209
  time to fit residues: 18.3326
Evaluate side-chains
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0570
   chunk 22 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0870
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.2634

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

Flipped N/Q/H residues before XYZ refinement:
** A 489 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.173940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146085 restraints weight = 5467.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150387 restraints weight = 2966.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153179 restraints weight = 2028.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4029  Z= 0.173
  Angle     :  0.638  12.070   5487  Z= 0.315
  Chirality :  0.041   0.208    629
  Planarity :  0.005   0.039    680
  Dihedral  :  4.294  21.127    540
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 25.12 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.41), residues: 492
  helix:  2.20 (0.26), residues: 383
  sheet: -1.66 (1.85), residues: 10
  loop : -0.83 (0.82), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.019   0.001   PHE A 527 
 TYR   0.010   0.001   TYR A 560 
 ARG   0.006   0.001   ARG A 429 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8734 (t0) cc_final: 0.8398 (t0)
REVERT: A  328 TYR cc_start: 0.8908 (t80) cc_final: 0.8577 (t80)
REVERT: A  335 TYR cc_start: 0.8562 (m-10) cc_final: 0.8323 (m-10)
REVERT: A  449 TYR cc_start: 0.7353 (m-80) cc_final: 0.7133 (m-80)
REVERT: A  552 LEU cc_start: 0.8581 (tp) cc_final: 0.8354 (tt)
REVERT: A  561 GLU cc_start: 0.8382 (tp30) cc_final: 0.8043 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1151
  time to fit residues: 17.1190
Evaluate side-chains
  111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  428 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 489 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.170285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.142621 restraints weight = 5494.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.146715 restraints weight = 2971.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149309 restraints weight = 2035.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4029  Z= 0.228
  Angle     :  0.662  10.865   5487  Z= 0.329
  Chirality :  0.041   0.199    629
  Planarity :  0.006   0.093    680
  Dihedral  :  4.341  21.005    540
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 25.84 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.41), residues: 492
  helix:  2.20 (0.26), residues: 382
  sheet: -1.51 (1.94), residues: 10
  loop : -0.88 (0.80), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.032   0.002   PHE A 527 
 TYR   0.011   0.001   TYR A 156 
 ARG   0.005   0.000   ARG A 429 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7910 (m-30) cc_final: 0.7553 (t0)
REVERT: A  185 ASP cc_start: 0.8741 (t0) cc_final: 0.8401 (t0)
REVERT: A  328 TYR cc_start: 0.8953 (t80) cc_final: 0.8454 (t80)
REVERT: A  335 TYR cc_start: 0.8643 (m-10) cc_final: 0.8332 (m-10)
REVERT: A  561 GLU cc_start: 0.8367 (tp30) cc_final: 0.8047 (tm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1097
  time to fit residues: 15.6525
Evaluate side-chains
  107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 489 GLN ** 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 = 0.3938 r_free = 0.3938 target = 0.170035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.142598 restraints weight = 5395.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.146546 restraints weight = 2918.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.149379 restraints weight = 2005.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4029  Z= 0.211
  Angle     :  0.650   9.534   5487  Z= 0.325
  Chirality :  0.041   0.180    629
  Planarity :  0.005   0.068    680
  Dihedral  :  4.340  18.989    540
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 27.51 %
    Favored  : 69.14 %
  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:  2.33 (0.41), residues: 492
  helix:  2.19 (0.26), residues: 383
  sheet: -1.28 (1.98), residues: 10
  loop : -0.75 (0.81), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  30 
 HIS   0.001   0.001   HIS A 341 
 PHE   0.017   0.001   PHE A 496 
 TYR   0.016   0.001   TYR A 156 
 ARG   0.007   0.001   ARG A 429 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7919 (m-30) cc_final: 0.7546 (t0)
REVERT: A  185 ASP cc_start: 0.8722 (t0) cc_final: 0.8370 (t0)
REVERT: A  335 TYR cc_start: 0.8614 (m-10) cc_final: 0.8361 (m-10)
REVERT: A  449 TYR cc_start: 0.7351 (m-80) cc_final: 0.7134 (m-80)
REVERT: A  454 SER cc_start: 0.8214 (t) cc_final: 0.7933 (t)
REVERT: A  561 GLU cc_start: 0.8373 (tp30) cc_final: 0.8059 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1152
  time to fit residues: 17.1029
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0170
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 489 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.172460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144804 restraints weight = 5440.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.149023 restraints weight = 2916.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151597 restraints weight = 1991.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4029  Z= 0.187
  Angle     :  0.637   9.253   5487  Z= 0.318
  Chirality :  0.040   0.162    629
  Planarity :  0.005   0.056    680
  Dihedral  :  4.302  20.699    540
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.71 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.41), residues: 492
  helix:  2.25 (0.26), residues: 383
  sheet: -1.04 (1.95), residues: 10
  loop : -0.63 (0.82), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  92 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.016   0.001   PHE A 496 
 TYR   0.009   0.001   TYR A 324 
 ARG   0.007   0.001   ARG A  31 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7902 (m-30) cc_final: 0.7545 (t0)
REVERT: A  185 ASP cc_start: 0.8739 (t0) cc_final: 0.8373 (t0)
REVERT: A  303 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: A  335 TYR cc_start: 0.8603 (m-10) cc_final: 0.8261 (m-10)
REVERT: A  449 TYR cc_start: 0.7339 (m-80) cc_final: 0.7100 (m-80)
REVERT: A  454 SER cc_start: 0.8257 (t) cc_final: 0.7976 (t)
REVERT: A  561 GLU cc_start: 0.8390 (tp30) cc_final: 0.8036 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1130
  time to fit residues: 16.7480
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0060
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.171653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.144358 restraints weight = 5479.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148562 restraints weight = 2927.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151444 restraints weight = 1991.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4029  Z= 0.198
  Angle     :  0.651   9.282   5487  Z= 0.326
  Chirality :  0.041   0.173    629
  Planarity :  0.005   0.055    680
  Dihedral  :  4.282  19.192    540
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.69 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 29.43 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.41), residues: 492
  helix:  2.23 (0.26), residues: 383
  sheet: -0.87 (1.91), residues: 10
  loop : -0.70 (0.82), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  92 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.015   0.001   PHE A 496 
 TYR   0.010   0.001   TYR A 156 
 ARG   0.011   0.001   ARG A  31 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7890 (m-30) cc_final: 0.7543 (t0)
REVERT: A  185 ASP cc_start: 0.8736 (t0) cc_final: 0.8404 (t0)
REVERT: A  335 TYR cc_start: 0.8641 (m-10) cc_final: 0.8277 (m-10)
REVERT: A  449 TYR cc_start: 0.7418 (m-80) cc_final: 0.7194 (m-80)
REVERT: A  454 SER cc_start: 0.8182 (t) cc_final: 0.7910 (t)
REVERT: A  561 GLU cc_start: 0.8378 (tp30) cc_final: 0.8018 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1097
  time to fit residues: 16.6681
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0570
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 489 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.172587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.145126 restraints weight = 5314.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149368 restraints weight = 2881.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151934 restraints weight = 1964.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4029  Z= 0.195
  Angle     :  0.684  12.001   5487  Z= 0.335
  Chirality :  0.041   0.181    629
  Planarity :  0.006   0.069    680
  Dihedral  :  4.325  21.480    540
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 29.43 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.41), residues: 492
  helix:  2.25 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.98 (0.75), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  92 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.015   0.001   PHE A 496 
 TYR   0.009   0.001   TYR A 324 
 ARG   0.015   0.001   ARG A  31 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1429.33 seconds
wall clock time: 26 minutes 44.89 seconds (1604.89 seconds total)