Starting phenix.real_space_refine
on Wed Sep 17 05:37:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7awa_11928/09_2025/7awa_11928.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    1667      2.51       5
     N     451      2.21       5
     O     477      1.98       5
     H    2703      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5310
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 5310
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 16, 'TRANS': 311}
  Time building chain proxies: 1.28, per 1000 atoms: 0.24
  Number of scatterers: 5310
  At special positions: 0
  Unit cell: (69.12, 74.52, 73.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O     477      8.00
     N     451      7.00
     C    1667      6.00
     H    2703      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 118.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  622

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      53.7% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 359 through 362
      removed outlier: 3.710A  pdb=" N   HIS A 362 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 359 through 362'
    Processing helix  chain 'A' and resid 365 through 382
      removed outlier: 3.757A  pdb=" N   ASP A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLU A 379 " --> pdb=" O   TRP A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 440
    Processing helix  chain 'A' and resid 447 through 457
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.634A  pdb=" N   SER A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ARG A 478 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
      removed outlier: 3.727A  pdb=" N   GLU A 482 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE A 484 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 497
      removed outlier: 3.869A  pdb=" N   ARG A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR A 491 " --> pdb=" O   GLN A 487 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU A 497 " --> pdb=" O   MET A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
      removed outlier: 3.776A  pdb=" N   GLU A 506 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.520A  pdb=" N   ILE A 516 " --> pdb=" O   PRO A 512 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLU A 518 " --> pdb=" O   ASN A 514 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLU A 526 " --> pdb=" O   ARG A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 544
      removed outlier: 3.605A  pdb=" N   ILE A 536 " --> pdb=" O   ASP A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 547
      No H-bonds generated for 'chain 'A' and resid 545 through 547'
    Processing helix  chain 'A' and resid 549 through 560
      removed outlier: 3.869A  pdb=" N   GLU A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA A 560 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 570
      removed outlier: 4.567A  pdb=" N   ARG A 568 " --> pdb=" O   HIS A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 574
      removed outlier: 3.723A  pdb=" N   LYS A 574 " --> pdb=" O   PRO A 571 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 571 through 574'
    Processing helix  chain 'A' and resid 582 through 594
      removed outlier: 3.924A  pdb=" N   ARG A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 621
      removed outlier: 5.242A  pdb=" N   GLN A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 643
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392
      removed outlier: 6.997A  pdb=" N   LEU A 353 " --> pdb=" O   ASN A 389 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   GLU A 391 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU A 355 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE A 410 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A 404 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 423
    Processing sheet with id=AA3, first strand: chain 'A' and resid 576 through 578

    105 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2700
        1.03 -     1.23: 8
        1.23 -     1.42: 1034
        1.42 -     1.62: 1591
        1.62 -     1.81: 21
  Bond restraints: 5354
  Sorted by residual:
  bond pdb=" N   SER A 345 "
       pdb=" H   SER A 345 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.65e+00
  bond pdb=" N   VAL A 347 "
       pdb=" CA  VAL A 347 "
    ideal  model  delta    sigma   weight residual
    1.468  1.495 -0.027 1.05e-02 9.07e+03 6.40e+00
  bond pdb=" N   MET A 346 "
       pdb=" H   MET A 346 "
    ideal  model  delta    sigma   weight residual
    0.860  0.910 -0.050 2.00e-02 2.50e+03 6.29e+00
  bond pdb=" N   VAL A 347 "
       pdb=" H   VAL A 347 "
    ideal  model  delta    sigma   weight residual
    0.860  0.908 -0.048 2.00e-02 2.50e+03 5.68e+00
  bond pdb=" C   VAL A 347 "
       pdb=" N   PRO A 348 "
    ideal  model  delta    sigma   weight residual
    1.331  1.356 -0.026 1.31e-02 5.83e+03 3.79e+00
  ... (remaining 5349 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 9325
        1.33 -     2.66: 380
        2.66 -     4.00: 29
        4.00 -     5.33: 4
        5.33 -     6.66: 2
  Bond angle restraints: 9740
  Sorted by residual:
  angle pdb=" CA  PRO A 348 "
        pdb=" C   PRO A 348 "
        pdb=" O   PRO A 348 "
      ideal   model   delta    sigma   weight residual
     121.67  116.09    5.58 1.22e+00 6.72e-01 2.09e+01
  angle pdb=" CA  PRO A 348 "
        pdb=" C   PRO A 348 "
        pdb=" N   GLY A 349 "
      ideal   model   delta    sigma   weight residual
     115.16  119.79   -4.63 1.28e+00 6.10e-01 1.31e+01
  angle pdb=" CA  VAL A 347 "
        pdb=" C   VAL A 347 "
        pdb=" O   VAL A 347 "
      ideal   model   delta    sigma   weight residual
     119.62  117.33    2.29 9.00e-01 1.23e+00 6.46e+00
  angle pdb=" N   GLU A 591 "
        pdb=" CA  GLU A 591 "
        pdb=" CB  GLU A 591 "
      ideal   model   delta    sigma   weight residual
     110.30  113.69   -3.39 1.54e+00 4.22e-01 4.84e+00
  angle pdb=" CA  VAL A 409 "
        pdb=" C   VAL A 409 "
        pdb=" N   PHE A 410 "
      ideal   model   delta    sigma   weight residual
     116.60  119.77   -3.17 1.45e+00 4.76e-01 4.77e+00
  ... (remaining 9735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 2224
       17.81 -    35.62: 188
       35.62 -    53.43: 49
       53.43 -    71.24: 14
       71.24 -    89.05: 3
  Dihedral angle restraints: 2478
    sinusoidal: 1410
      harmonic: 1068
  Sorted by residual:
  dihedral pdb=" CA  ALA A 624 "
           pdb=" C   ALA A 624 "
           pdb=" N   LYS A 625 "
           pdb=" CA  LYS A 625 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ARG A 607 "
           pdb=" C   ARG A 607 "
           pdb=" N   HIS A 608 "
           pdb=" CA  HIS A 608 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.32   15.68     0      5.00e+00 4.00e-02 9.83e+00
  dihedral pdb=" CA  ARG A 563 "
           pdb=" CB  ARG A 563 "
           pdb=" CG  ARG A 563 "
           pdb=" CD  ARG A 563 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.89   58.89     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 2475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 274
       0.031 -    0.062: 99
       0.062 -    0.093: 29
       0.093 -    0.124: 22
       0.124 -    0.155: 3
  Chirality restraints: 427
  Sorted by residual:
  chirality pdb=" CB  VAL A 347 "
            pdb=" CA  VAL A 347 "
            pdb=" CG1 VAL A 347 "
            pdb=" CG2 VAL A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  VAL A 347 "
            pdb=" N   VAL A 347 "
            pdb=" C   VAL A 347 "
            pdb=" CB  VAL A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE A 651 "
            pdb=" N   ILE A 651 "
            pdb=" C   ILE A 651 "
            pdb=" CB  ILE A 651 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 424 not shown)

  Planarity restraints: 767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 371 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   ASP A 371 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A 371 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A 372 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 395 "   -0.023 5.00e-02 4.00e+02   3.50e-02 1.97e+00
        pdb=" N   PRO A 396 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 396 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 396 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 649 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO A 650 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 650 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 650 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 764 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.24: 607
        2.24 -     2.83: 11947
        2.83 -     3.42: 12807
        3.42 -     4.01: 17007
        4.01 -     4.60: 26376
  Nonbonded interactions: 68744
  Sorted by model distance:
  nonbonded pdb=" HE  ARG A 356 "
            pdb=" OE1 GLU A 391 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" O   LEU A 355 "
            pdb=" H   GLU A 391 "
     model   vdw
     1.664 2.450
  nonbonded pdb=" O   LEU A 476 "
            pdb=" H   HIS A 479 "
     model   vdw
     1.680 2.450
  nonbonded pdb=" O   THR A 642 "
            pdb=" H   THR A 645 "
     model   vdw
     1.723 2.450
  nonbonded pdb=" OE1 GLU A 656 "
            pdb=" H   GLU A 656 "
     model   vdw
     1.738 2.450
  ... (remaining 68739 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  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:             0.040
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.790
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
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   0.029   2651  Z= 0.180
  Angle     :  0.637   6.660   3592  Z= 0.380
  Chirality :  0.042   0.155    427
  Planarity :  0.004   0.035    456
  Dihedral  : 14.223  89.047   1016
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.43), residues: 326
  helix: -0.95 (0.42), residues: 140
  sheet: -1.81 (0.75), residues: 35
  loop : -2.32 (0.47), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 478 
 TYR   0.012   0.002   TYR A 420 
 PHE   0.007   0.001   PHE A 483 
 TRP   0.005   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2651)
  covalent geometry    : angle       0.63735 ( 3592)
  hydrogen bonds       : bond        0.17106 (  105)
  hydrogen bonds       : angle       6.52364 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  18 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1987
  time to fit residues: 4.1512
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   overall best weight:    2.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.095467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063709 restraints weight = 21885.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.067018 restraints weight = 9533.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.068924 restraints weight = 6239.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.069921 restraints weight = 5103.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.070277 restraints weight = 4651.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2651  Z= 0.193
  Angle     :  0.576   5.425   3592  Z= 0.304
  Chirality :  0.042   0.127    427
  Planarity :  0.004   0.039    456
  Dihedral  :  5.198  21.717    357
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.47 (0.43), residues: 326
  helix: -0.65 (0.42), residues: 145
  sheet: -2.03 (0.71), residues: 35
  loop : -2.57 (0.46), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.009   0.001   TYR A 420 
 PHE   0.010   0.001   PHE A 637 
 TRP   0.004   0.001   TRP A 654 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 2651)
  covalent geometry    : angle       0.57647 ( 3592)
  hydrogen bonds       : bond        0.04356 (  105)
  hydrogen bonds       : angle       5.48677 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  440 MET cc_start: 0.7939 (mtp) cc_final: 0.7639 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.2566
  time to fit residues: 4.6902
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.096768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.065464 restraints weight = 21580.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.068760 restraints weight = 9201.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.070706 restraints weight = 5977.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.071747 restraints weight = 4855.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.071840 restraints weight = 4399.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2651  Z= 0.106
  Angle     :  0.513   3.854   3592  Z= 0.266
  Chirality :  0.040   0.137    427
  Planarity :  0.004   0.036    456
  Dihedral  :  4.888  19.378    357
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.84 %
    Favored  : 93.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.44), residues: 326
  helix: -0.23 (0.43), residues: 145
  sheet: -2.11 (0.69), residues: 37
  loop : -2.41 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.006   0.001   TYR A 420 
 PHE   0.008   0.001   PHE A 637 
 TRP   0.005   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2651)
  covalent geometry    : angle       0.51296 ( 3592)
  hydrogen bonds       : bond        0.03354 (  105)
  hydrogen bonds       : angle       4.86311 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  20 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 MET cc_start: 0.6010 (tpt) cc_final: 0.5530 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.2942
  time to fit residues: 6.5656
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.097132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.065517 restraints weight = 21226.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.068760 restraints weight = 9154.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.070621 restraints weight = 6006.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071618 restraints weight = 4930.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.071947 restraints weight = 4489.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2651  Z= 0.111
  Angle     :  0.494   3.756   3592  Z= 0.257
  Chirality :  0.040   0.127    427
  Planarity :  0.004   0.036    456
  Dihedral  :  4.681  19.144    357
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  7.90 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.45), residues: 326
  helix:  0.02 (0.44), residues: 146
  sheet: -1.87 (0.71), residues: 35
  loop : -2.33 (0.46), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.005   0.001   TYR A 420 
 PHE   0.006   0.001   PHE A 457 
 TRP   0.004   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2651)
  covalent geometry    : angle       0.49436 ( 3592)
  hydrogen bonds       : bond        0.03155 (  105)
  hydrogen bonds       : angle       4.61912 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  17 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 17
  average time/residue: 0.2546
  time to fit residues: 4.9848
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.097163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.065672 restraints weight = 21593.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.068844 restraints weight = 9212.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.070756 restraints weight = 6019.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.071762 restraints weight = 4928.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.071953 restraints weight = 4488.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2651  Z= 0.110
  Angle     :  0.491   3.816   3592  Z= 0.252
  Chirality :  0.040   0.140    427
  Planarity :  0.003   0.035    456
  Dihedral  :  4.528  18.282    357
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.87 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.45), residues: 326
  helix:  0.28 (0.45), residues: 146
  sheet: -1.80 (0.71), residues: 35
  loop : -2.21 (0.47), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.005   0.001   TYR A 420 
 PHE   0.005   0.001   PHE A 457 
 TRP   0.003   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2651)
  covalent geometry    : angle       0.49137 ( 3592)
  hydrogen bonds       : bond        0.02965 (  105)
  hydrogen bonds       : angle       4.46551 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  18 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 MET cc_start: 0.6043 (tpt) cc_final: 0.5554 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 18
  average time/residue: 0.2367
  time to fit residues: 4.8714
Evaluate side-chains
  16 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 1 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0570
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.5498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.098568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.067102 restraints weight = 21283.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.070410 restraints weight = 9042.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.072377 restraints weight = 5916.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072982 restraints weight = 4825.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.073772 restraints weight = 4485.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2651  Z= 0.078
  Angle     :  0.460   3.436   3592  Z= 0.233
  Chirality :  0.039   0.138    427
  Planarity :  0.003   0.033    456
  Dihedral  :  4.259  16.908    357
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.56 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.46), residues: 326
  helix:  0.65 (0.46), residues: 142
  sheet: -1.68 (0.72), residues: 35
  loop : -1.88 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.003   0.000   TYR A 420 
 PHE   0.005   0.001   PHE A 457 
 TRP   0.005   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 ( 2651)
  covalent geometry    : angle       0.46036 ( 3592)
  hydrogen bonds       : bond        0.02314 (  105)
  hydrogen bonds       : angle       4.19578 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  21 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7414 (mp0)
REVERT: A  598 MET cc_start: 0.5816 (tpt) cc_final: 0.5384 (tpt)
  outliers start: 3
  outliers final: 1
  residues processed: 21
  average time/residue: 0.2131
  time to fit residues: 5.1702
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 8 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.096643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.064130 restraints weight = 21585.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.067302 restraints weight = 9558.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.069118 restraints weight = 6353.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.070078 restraints weight = 5244.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.070455 restraints weight = 4786.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2651  Z= 0.181
  Angle     :  0.509   4.227   3592  Z= 0.266
  Chirality :  0.041   0.132    427
  Planarity :  0.004   0.033    456
  Dihedral  :  4.494  18.362    357
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  7.90 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.46), residues: 326
  helix:  0.50 (0.45), residues: 147
  sheet: -1.66 (0.72), residues: 35
  loop : -2.03 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.009   0.001   TYR A 420 
 PHE   0.007   0.001   PHE A 483 
 TRP   0.004   0.001   TRP A 654 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 2651)
  covalent geometry    : angle       0.50921 ( 3592)
  hydrogen bonds       : bond        0.03473 (  105)
  hydrogen bonds       : angle       4.59346 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7519 (mp0)
REVERT: A  552 MET cc_start: 0.8105 (mmm) cc_final: 0.7901 (mmm)
REVERT: A  598 MET cc_start: 0.5901 (tpt) cc_final: 0.5472 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 19
  average time/residue: 0.2481
  time to fit residues: 5.4345
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.097461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.065101 restraints weight = 21182.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.068308 restraints weight = 9339.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.070135 restraints weight = 6197.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.071093 restraints weight = 5119.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.071252 restraints weight = 4675.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2651  Z= 0.114
  Angle     :  0.473   3.553   3592  Z= 0.244
  Chirality :  0.040   0.136    427
  Planarity :  0.003   0.032    456
  Dihedral  :  4.373  17.167    357
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.25 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.46), residues: 326
  helix:  0.75 (0.45), residues: 143
  sheet: -1.63 (0.73), residues: 35
  loop : -1.86 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.005   0.001   TYR A 420 
 PHE   0.005   0.001   PHE A 457 
 TRP   0.002   0.000   TRP A 445 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2651)
  covalent geometry    : angle       0.47268 ( 3592)
  hydrogen bonds       : bond        0.02884 (  105)
  hydrogen bonds       : angle       4.37549 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: A  598 MET cc_start: 0.5856 (tpt) cc_final: 0.5416 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 19
  average time/residue: 0.2452
  time to fit residues: 5.3965
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.097443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.065107 restraints weight = 21388.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.068355 restraints weight = 9355.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.070198 restraints weight = 6167.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.071178 restraints weight = 5076.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.071344 restraints weight = 4632.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2651  Z= 0.109
  Angle     :  0.475   5.688   3592  Z= 0.242
  Chirality :  0.040   0.144    427
  Planarity :  0.003   0.033    456
  Dihedral  :  4.269  16.762    357
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.59 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.47), residues: 326
  helix:  0.92 (0.46), residues: 143
  sheet: -1.62 (0.72), residues: 35
  loop : -1.80 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.006   0.001   TYR A 420 
 PHE   0.005   0.001   PHE A 457 
 TRP   0.004   0.001   TRP A 654 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2651)
  covalent geometry    : angle       0.47518 ( 3592)
  hydrogen bonds       : bond        0.02746 (  105)
  hydrogen bonds       : angle       4.28930 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7499 (mp0)
REVERT: A  598 MET cc_start: 0.5813 (tpt) cc_final: 0.5395 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 19
  average time/residue: 0.2421
  time to fit residues: 5.2637
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   overall best weight:    2.0788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.097002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.064560 restraints weight = 21337.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.067759 restraints weight = 9414.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.069571 restraints weight = 6236.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.070211 restraints weight = 5143.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.070805 restraints weight = 4770.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2651  Z= 0.155
  Angle     :  0.502   5.156   3592  Z= 0.260
  Chirality :  0.040   0.131    427
  Planarity :  0.004   0.033    456
  Dihedral  :  4.393  17.431    357
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.59 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.47), residues: 326
  helix:  0.72 (0.45), residues: 147
  sheet: -1.60 (0.74), residues: 35
  loop : -1.93 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.006   0.001   TYR A 420 
 PHE   0.005   0.001   PHE A 483 
 TRP   0.003   0.001   TRP A 654 
 HIS   0.001   0.000   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 2651)
  covalent geometry    : angle       0.50203 ( 3592)
  hydrogen bonds       : bond        0.03250 (  105)
  hydrogen bonds       : angle       4.46694 (  306)

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

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

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  652 Ramachandran restraints generated.
    326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  579 is missing expected H atoms. Skipping.
Evaluate side-chains
  19 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 MET cc_start: 0.5825 (tpt) cc_final: 0.5418 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 19
  average time/residue: 0.2365
  time to fit residues: 5.1961
Evaluate side-chains
  18 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.098539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.066305 restraints weight = 21385.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.069561 restraints weight = 9311.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071446 restraints weight = 6154.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.072424 restraints weight = 5055.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.072589 restraints weight = 4614.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2651  Z= 0.090
  Angle     :  0.469   5.597   3592  Z= 0.238
  Chirality :  0.040   0.165    427
  Planarity :  0.003   0.033    456
  Dihedral  :  4.194  16.088    357
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  8.59 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.47), residues: 326
  helix:  0.95 (0.46), residues: 144
  sheet: -1.12 (0.80), residues: 28
  loop : -1.77 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.004   0.000   TYR A 420 
 PHE   0.005   0.001   PHE A 457 
 TRP   0.003   0.001   TRP A 445 
 HIS   0.001   0.000   HIS A 564 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 2651)
  covalent geometry    : angle       0.46910 ( 3592)
  hydrogen bonds       : bond        0.02518 (  105)
  hydrogen bonds       : angle       4.18142 (  306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.87 seconds
wall clock time: 25 minutes 56.88 seconds (1556.88 seconds total)