Starting phenix.real_space_refine
on Thu Jun  5 09:45:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oo6_17005/06_2025/8oo6_17005.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P      54      5.49       5
     Mg      1      5.21       5
     S      15      5.16       5
     C    3549      2.51       5
     N    1042      2.21       5
     O    1229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5890
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 604, 4782
          Classifications: {'peptide': 604}
          Link IDs: {'PTRANS': 28, 'TRANS': 575}
    Chain: "T"
      Number of atoms: 555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 555
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "P"
      Number of atoms: 366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 366
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "D"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 186
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.40, per 1000 atoms: 1.43
  Number of scatterers: 5890
  At special positions: 0
  Unit cell: (86.6, 96.992, 78.806, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      15     16.00
     P      54     15.00
     Mg      1     11.99
     O    1229      8.00
     N    1042      7.00
     C    3549      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.66
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 3 sheets defined
      59.8% alpha, 7.5% beta
      27 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 3.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 335 through 347
    Processing helix  chain 'A' and resid 397 through 410
      Proline residue:  A 407  - end of helix
    Processing helix  chain 'A' and resid 420 through 431
      removed outlier: 3.659A  pdb=" N   TYR A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
    Processing helix  chain 'A' and resid 457 through 466
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 4.010A  pdb=" N   ILE A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 489
      removed outlier: 3.755A  pdb=" N   ILE A 489 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 517
      removed outlier: 3.587A  pdb=" N   ALA A 494 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
      Proline residue:  A 514  - end of helix
    Processing helix  chain 'A' and resid 520 through 529
    Processing helix  chain 'A' and resid 532 through 544
      removed outlier: 4.231A  pdb=" N   VAL A 536 " --> pdb=" O   PRO A 532 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY A 544 " --> pdb=" O   ILE A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 575
      removed outlier: 3.886A  pdb=" N   LEU A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A 557 " --> pdb=" O   HIS A 553 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU A 558 " --> pdb=" O   ASN A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 594
    Processing helix  chain 'A' and resid 610 through 618
    Processing helix  chain 'A' and resid 621 through 644
      removed outlier: 4.350A  pdb=" N   LYS A 625 " --> pdb=" O   TYR A 621 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A 641 " --> pdb=" O   LYS A 637 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ASP A 642 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 693
      removed outlier: 3.841A  pdb=" N   PHE A 693 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'A' and resid 720 through 730
    Processing helix  chain 'A' and resid 732 through 743
      removed outlier: 3.933A  pdb=" N   ALA A 738 " --> pdb=" O   HIS A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 766
    Processing helix  chain 'A' and resid 769 through 778
    Processing helix  chain 'A' and resid 780 through 795
    Processing helix  chain 'A' and resid 795 through 813
      removed outlier: 3.650A  pdb=" N   LEU A 799 " --> pdb=" O   TYR A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 871
      removed outlier: 3.551A  pdb=" N   ALA A 838 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      Proline residue:  A 847  - end of helix
    Processing helix  chain 'A' and resid 893 through 906
    Processing helix  chain 'A' and resid 923 through 928
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332
      removed outlier: 7.130A  pdb=" N   VAL A 331 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 371 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A 352 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LYS A 416 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 875 through 880
      removed outlier: 3.548A  pdb=" N   ILE A 877 " --> pdb=" O   VAL A 885 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   VAL A 885 " --> pdb=" O   ILE A 877 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLN A 879 " --> pdb=" O   GLU A 883 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU A 883 " --> pdb=" O   GLN A 879 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL A 702 " --> pdb=" O   PHE A 886 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 816

    261 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1376
        1.33 -     1.45: 1384
        1.45 -     1.57: 3217
        1.57 -     1.69: 105
        1.69 -     1.81: 29
  Bond restraints: 6111
  Sorted by residual:
  bond pdb=" CA  VAL A 452 "
       pdb=" CB  VAL A 452 "
    ideal  model  delta    sigma   weight residual
    1.527  1.545 -0.018 1.31e-02 5.83e+03 1.86e+00
  bond pdb=" CG  LEU A 449 "
       pdb=" CD1 LEU A 449 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.60e+00
  bond pdb=" CB  ASP A 388 "
       pdb=" CG  ASP A 388 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.16e+00
  bond pdb=" CB  PRO A 674 "
       pdb=" CG  PRO A 674 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.07e+00
  bond pdb=" CB  LEU A 449 "
       pdb=" CG  LEU A 449 "
    ideal  model  delta    sigma   weight residual
    1.530  1.510  0.020 2.00e-02 2.50e+03 9.98e-01
  ... (remaining 6106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 8235
        1.71 -     3.41: 220
        3.41 -     5.12: 37
        5.12 -     6.83: 3
        6.83 -     8.54: 4
  Bond angle restraints: 8499
  Sorted by residual:
  angle pdb=" N   GLU A 629 "
        pdb=" CA  GLU A 629 "
        pdb=" CB  GLU A 629 "
      ideal   model   delta    sigma   weight residual
     110.12  114.36   -4.24 1.47e+00 4.63e-01 8.33e+00
  angle pdb=" CB  MET A 714 "
        pdb=" CG  MET A 714 "
        pdb=" SD  MET A 714 "
      ideal   model   delta    sigma   weight residual
     112.70  104.16    8.54 3.00e+00 1.11e-01 8.10e+00
  angle pdb=" N   ALA A 366 "
        pdb=" CA  ALA A 366 "
        pdb=" C   ALA A 366 "
      ideal   model   delta    sigma   weight residual
     111.17  115.17   -4.00 1.41e+00 5.03e-01 8.06e+00
  angle pdb=" N   GLN A 507 "
        pdb=" CA  GLN A 507 "
        pdb=" CB  GLN A 507 "
      ideal   model   delta    sigma   weight residual
     110.28  114.56   -4.28 1.55e+00 4.16e-01 7.62e+00
  angle pdb=" N   MET A 802 "
        pdb=" CA  MET A 802 "
        pdb=" CB  MET A 802 "
      ideal   model   delta    sigma   weight residual
     110.12  113.89   -3.77 1.47e+00 4.63e-01 6.59e+00
  ... (remaining 8494 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 2887
       17.99 -    35.98: 419
       35.98 -    53.96: 215
       53.96 -    71.95: 41
       71.95 -    89.94: 7
  Dihedral angle restraints: 3569
    sinusoidal: 1806
      harmonic: 1763
  Sorted by residual:
  dihedral pdb=" CA  ASP A 705 "
           pdb=" C   ASP A 705 "
           pdb=" N   TYR A 706 "
           pdb=" CA  TYR A 706 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  LEU A 346 "
           pdb=" C   LEU A 346 "
           pdb=" N   GLU A 347 "
           pdb=" CA  GLU A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  GLU A 611 "
           pdb=" C   GLU A 611 "
           pdb=" N   GLU A 612 "
           pdb=" CA  GLU A 612 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 3566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 678
       0.035 -    0.070: 185
       0.070 -    0.106: 79
       0.106 -    0.141: 10
       0.141 -    0.176: 4
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CA  MET A 531 "
            pdb=" N   MET A 531 "
            pdb=" C   MET A 531 "
            pdb=" CB  MET A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CG  LEU A 884 "
            pdb=" CB  LEU A 884 "
            pdb=" CD1 LEU A 884 "
            pdb=" CD2 LEU A 884 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  GLN A 507 "
            pdb=" N   GLN A 507 "
            pdb=" C   GLN A 507 "
            pdb=" CB  GLN A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 953 not shown)

  Planarity restraints: 916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 465 "    0.017 2.00e-02 2.50e+03   1.47e-02 5.39e+00
        pdb=" CG  TRP A 465 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 465 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 465 "   -0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 465 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 465 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 465 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 465 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 465 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 465 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 392 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 393 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 393 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 393 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 388 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" C   ASP A 388 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASP A 388 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 389 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 913 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 910
        2.76 -     3.29: 5838
        3.29 -     3.83: 10831
        3.83 -     4.36: 12008
        4.36 -     4.90: 19050
  Nonbonded interactions: 48637
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 485 "
            pdb=" OD1 ASN A 487 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG1 THR A 358 "
            pdb=" O   ASN A 367 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" ND2 ASN A 579 "
            pdb=" OP1  DA T  27 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   GLN A 868 "
            pdb=" NE2 GLN A 871 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" NH2 ARG A 909 "
            pdb=" O   LEU A 910 "
     model   vdw
     2.313 3.120
  ... (remaining 48632 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             5.240
  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:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     30.260
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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   0.052   6111  Z= 0.159
  Angle     :  0.667   8.537   8499  Z= 0.374
  Chirality :  0.039   0.176    956
  Planarity :  0.004   0.054    916
  Dihedral  : 20.164  89.936   2429
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.35), residues: 602
  helix:  0.78 (0.29), residues: 321
  sheet: -1.17 (0.85), residues: 41
  loop : -0.92 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 465 
 HIS   0.003   0.001   HIS A 734 
 PHE   0.022   0.001   PHE A 762 
 TYR   0.012   0.001   TYR A 801 
 ARG   0.003   0.000   ARG A 781 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11618 (  331)
  hydrogen bonds       : angle       6.09963 (  911)
  covalent geometry    : bond        0.00321 ( 6111)
  covalent geometry    : angle       0.66705 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.9011 (mt) cc_final: 0.8758 (mt)
REVERT: A  798 VAL cc_start: 0.9432 (t) cc_final: 0.9063 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1787
  time to fit residues: 9.6642
Evaluate side-chains
  24 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 25 optimal weight:    0.1980
   chunk 49 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 488 GLN
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 528 ASN
A 761 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.055523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.044548 restraints weight = 38385.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045813 restraints weight = 21839.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.046647 restraints weight = 15008.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6111  Z= 0.131
  Angle     :  0.566   6.577   8499  Z= 0.315
  Chirality :  0.038   0.140    956
  Planarity :  0.004   0.051    916
  Dihedral  : 22.279  59.945   1234
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.36), residues: 602
  helix:  1.14 (0.30), residues: 329
  sheet: -0.71 (0.90), residues: 41
  loop : -1.19 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 465 
 HIS   0.003   0.001   HIS A 901 
 PHE   0.010   0.001   PHE A 762 
 TYR   0.008   0.001   TYR A 630 
 ARG   0.003   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  331)
  hydrogen bonds       : angle       4.68874 (  911)
  covalent geometry    : bond        0.00285 ( 6111)
  covalent geometry    : angle       0.56629 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.8976 (mt) cc_final: 0.8540 (mt)
REVERT: A  559 LEU cc_start: 0.8966 (mt) cc_final: 0.8739 (mt)
REVERT: A  798 VAL cc_start: 0.9436 (t) cc_final: 0.8827 (t)
REVERT: A  802 MET cc_start: 0.9173 (mpp) cc_final: 0.8926 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1261
  time to fit residues: 7.1120
Evaluate side-chains
  24 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
** A 507 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 = 0.3228 r_free = 0.3228 target = 0.054054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.043369 restraints weight = 38614.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.044662 restraints weight = 21481.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.045385 restraints weight = 14440.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6111  Z= 0.151
  Angle     :  0.579   6.918   8499  Z= 0.320
  Chirality :  0.039   0.165    956
  Planarity :  0.004   0.048    916
  Dihedral  : 22.220  59.755   1234
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.35), residues: 602
  helix:  1.03 (0.29), residues: 333
  sheet: -0.55 (0.89), residues: 41
  loop : -1.19 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 465 
 HIS   0.007   0.001   HIS A 928 
 PHE   0.009   0.001   PHE A 373 
 TYR   0.010   0.001   TYR A 795 
 ARG   0.004   0.000   ARG A 631 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  331)
  hydrogen bonds       : angle       4.52702 (  911)
  covalent geometry    : bond        0.00334 ( 6111)
  covalent geometry    : angle       0.57898 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A  343 ILE cc_start: 0.8595 (pt) cc_final: 0.8274 (pt)
REVERT: A  346 LEU cc_start: 0.9025 (mt) cc_final: 0.8600 (mt)
REVERT: A  798 VAL cc_start: 0.9394 (t) cc_final: 0.8994 (t)
REVERT: A  802 MET cc_start: 0.9211 (mpp) cc_final: 0.8988 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1269
  time to fit residues: 6.6939
Evaluate side-chains
  23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 56 optimal weight:    0.3980
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   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 488 GLN
** A 507 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 = 0.3239 r_free = 0.3239 target = 0.054345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.043306 restraints weight = 39043.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.044585 restraints weight = 22142.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045422 restraints weight = 15140.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6111  Z= 0.124
  Angle     :  0.566   6.366   8499  Z= 0.308
  Chirality :  0.038   0.156    956
  Planarity :  0.004   0.048    916
  Dihedral  : 22.200  59.765   1234
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.29 (0.35), residues: 602
  helix:  1.20 (0.29), residues: 329
  sheet: -0.46 (0.88), residues: 41
  loop : -1.14 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 924 
 HIS   0.003   0.001   HIS A 928 
 PHE   0.007   0.001   PHE A 373 
 TYR   0.010   0.001   TYR A 659 
 ARG   0.002   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  331)
  hydrogen bonds       : angle       4.37023 (  911)
  covalent geometry    : bond        0.00268 ( 6111)
  covalent geometry    : angle       0.56584 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9461 (t) cc_final: 0.8898 (t)
REVERT: A  802 MET cc_start: 0.9235 (mpp) cc_final: 0.8930 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1298
  time to fit residues: 6.7950
Evaluate side-chains
  20 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    0.0670
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.3924

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

Flipped N/Q/H residues before XYZ refinement:
A 456 HIS
A 488 GLN
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 845 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.050266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.039485 restraints weight = 39950.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.040652 restraints weight = 22707.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.041427 restraints weight = 15552.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6111  Z= 0.230
  Angle     :  0.667   8.730   8499  Z= 0.365
  Chirality :  0.041   0.170    956
  Planarity :  0.005   0.049    916
  Dihedral  : 22.381  65.219   1234
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.34), residues: 602
  helix:  0.71 (0.28), residues: 332
  sheet: -0.48 (0.85), residues: 41
  loop : -1.35 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 513 
 HIS   0.005   0.001   HIS A 327 
 PHE   0.013   0.002   PHE A 771 
 TYR   0.015   0.002   TYR A 795 
 ARG   0.004   0.001   ARG A 873 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05676 (  331)
  hydrogen bonds       : angle       4.70774 (  911)
  covalent geometry    : bond        0.00501 ( 6111)
  covalent geometry    : angle       0.66725 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  802 MET cc_start: 0.9223 (mpp) cc_final: 0.8857 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1291
  time to fit residues: 6.2068
Evaluate side-chains
  22 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    3.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.048527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.037974 restraints weight = 40683.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.039122 restraints weight = 22964.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.039873 restraints weight = 15858.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6111  Z= 0.237
  Angle     :  0.667   7.447   8499  Z= 0.370
  Chirality :  0.042   0.170    956
  Planarity :  0.005   0.080    916
  Dihedral  : 22.561  69.856   1234
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.44 (0.34), residues: 602
  helix:  0.52 (0.28), residues: 335
  sheet: -0.39 (0.84), residues: 41
  loop : -1.45 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 866 
 HIS   0.005   0.002   HIS A 716 
 PHE   0.011   0.002   PHE A 771 
 TYR   0.013   0.002   TYR A 787 
 ARG   0.003   0.000   ARG A 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05290 (  331)
  hydrogen bonds       : angle       4.82586 (  911)
  covalent geometry    : bond        0.00516 ( 6111)
  covalent geometry    : angle       0.66683 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  512 MET cc_start: 0.8907 (ttp) cc_final: 0.8655 (ttp)
REVERT: A  798 VAL cc_start: 0.9392 (t) cc_final: 0.8993 (t)
REVERT: A  802 MET cc_start: 0.9336 (mpp) cc_final: 0.8994 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1384
  time to fit residues: 5.7300
Evaluate side-chains
  21 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
A 845 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.050246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.039641 restraints weight = 39832.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.040808 restraints weight = 22500.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.041573 restraints weight = 15494.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6111  Z= 0.131
  Angle     :  0.581   7.060   8499  Z= 0.319
  Chirality :  0.039   0.133    956
  Planarity :  0.004   0.069    916
  Dihedral  : 22.470  71.504   1234
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.77 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.35), residues: 602
  helix:  1.01 (0.29), residues: 331
  sheet: -0.28 (0.85), residues: 41
  loop : -1.31 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 509 
 PHE   0.007   0.001   PHE A 727 
 TYR   0.011   0.001   TYR A 497 
 ARG   0.002   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  331)
  hydrogen bonds       : angle       4.31770 (  911)
  covalent geometry    : bond        0.00280 ( 6111)
  covalent geometry    : angle       0.58131 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9408 (t) cc_final: 0.8997 (t)
REVERT: A  802 MET cc_start: 0.9377 (mpp) cc_final: 0.9074 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 27
  average time/residue: 0.1376
  time to fit residues: 6.1389
Evaluate side-chains
  23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0060
   chunk 14 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
** A 507 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 = 0.3137 r_free = 0.3137 target = 0.050086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.039533 restraints weight = 40283.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.040684 restraints weight = 22846.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.041421 restraints weight = 15814.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6111  Z= 0.142
  Angle     :  0.596   6.145   8499  Z= 0.328
  Chirality :  0.039   0.173    956
  Planarity :  0.004   0.062    916
  Dihedral  : 22.363  72.453   1234
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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:  0.12 (0.35), residues: 602
  helix:  1.02 (0.29), residues: 334
  sheet: -0.19 (0.84), residues: 41
  loop : -1.27 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 342 
 HIS   0.002   0.001   HIS A 327 
 PHE   0.008   0.001   PHE A 771 
 TYR   0.009   0.001   TYR A 497 
 ARG   0.002   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04200 (  331)
  hydrogen bonds       : angle       4.39998 (  911)
  covalent geometry    : bond        0.00310 ( 6111)
  covalent geometry    : angle       0.59574 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A  512 MET cc_start: 0.8729 (ttp) cc_final: 0.8462 (ttp)
REVERT: A  798 VAL cc_start: 0.9374 (t) cc_final: 0.9016 (t)
REVERT: A  802 MET cc_start: 0.9381 (mpp) cc_final: 0.8993 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1258
  time to fit residues: 5.7396
Evaluate side-chains
  23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
** A 507 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 = 0.3151 r_free = 0.3151 target = 0.050594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.040012 restraints weight = 40259.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.041186 restraints weight = 22679.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.041942 restraints weight = 15613.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6111  Z= 0.132
  Angle     :  0.593   6.931   8499  Z= 0.324
  Chirality :  0.039   0.163    956
  Planarity :  0.004   0.056    916
  Dihedral  : 22.290  72.702   1234
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  0.26 (0.35), residues: 602
  helix:  1.14 (0.29), residues: 335
  sheet: -0.03 (0.84), residues: 41
  loop : -1.24 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 342 
 HIS   0.002   0.001   HIS A 734 
 PHE   0.007   0.001   PHE A 373 
 TYR   0.008   0.001   TYR A 497 
 ARG   0.003   0.000   ARG A 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  331)
  hydrogen bonds       : angle       4.38112 (  911)
  covalent geometry    : bond        0.00287 ( 6111)
  covalent geometry    : angle       0.59294 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 MET cc_start: 0.8707 (ttp) cc_final: 0.8448 (ttp)
REVERT: A  798 VAL cc_start: 0.9376 (t) cc_final: 0.9005 (t)
REVERT: A  802 MET cc_start: 0.9373 (mpp) cc_final: 0.8958 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1545
  time to fit residues: 6.7013
Evaluate side-chains
  24 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0030
   chunk 53 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.2994

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
A 845 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.050122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.039602 restraints weight = 40266.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.040761 restraints weight = 22698.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.041488 restraints weight = 15562.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6111  Z= 0.136
  Angle     :  0.591   6.327   8499  Z= 0.325
  Chirality :  0.039   0.135    956
  Planarity :  0.004   0.054    916
  Dihedral  : 22.258  73.116   1234
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.20 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.35), residues: 602
  helix:  1.03 (0.29), residues: 335
  sheet:  0.03 (0.85), residues: 41
  loop : -1.25 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 881 
 PHE   0.008   0.001   PHE A 771 
 TYR   0.017   0.001   TYR A 787 
 ARG   0.002   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  331)
  hydrogen bonds       : angle       4.40813 (  911)
  covalent geometry    : bond        0.00298 ( 6111)
  covalent geometry    : angle       0.59086 ( 8499)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 MET cc_start: 0.8767 (ttp) cc_final: 0.8495 (ttp)
REVERT: A  798 VAL cc_start: 0.9363 (t) cc_final: 0.8979 (t)
REVERT: A  802 MET cc_start: 0.9395 (mpp) cc_final: 0.8971 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1287
  time to fit residues: 5.8799
Evaluate side-chains
  23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.049012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.038566 restraints weight = 40613.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.039754 restraints weight = 22526.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.040522 restraints weight = 15236.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6111  Z= 0.163
  Angle     :  0.605   6.992   8499  Z= 0.333
  Chirality :  0.040   0.133    956
  Planarity :  0.004   0.051    916
  Dihedral  : 22.272  75.024   1234
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.35), residues: 602
  helix:  0.97 (0.29), residues: 334
  sheet: -0.03 (0.85), residues: 41
  loop : -1.32 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 327 
 PHE   0.010   0.001   PHE A 771 
 TYR   0.014   0.002   TYR A 787 
 ARG   0.003   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  331)
  hydrogen bonds       : angle       4.44879 (  911)
  covalent geometry    : bond        0.00359 ( 6111)
  covalent geometry    : angle       0.60453 ( 8499)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2212.20 seconds
wall clock time: 40 minutes 6.28 seconds (2406.28 seconds total)