Starting phenix.real_space_refine
on Tue Feb 11 13:53:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oo6_17005/02_2025/8oo6_17005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oo6_17005/02_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_17005/02_2025/8oo6_17005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oo6_17005/02_2025/8oo6_17005.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oo6_17005/02_2025/8oo6_17005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oo6_17005/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.83, per 1000 atoms: 0.82
  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: 1.52
  Conformation dependent library (CDL) restraints added in 803.7 milliseconds
  

  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: 2.23
  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: 2.18

  Time building geometry restraints manager: 1.74 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.690
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.610
-------------------------------------------------------------------------------
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= 0.203
  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 

*********************** 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  : 0.595 
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: 0.1589
  time to fit residues: 8.8851
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  : 0.654 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.055698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.044658 restraints weight = 38777.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.045950 restraints weight = 22119.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.046768 restraints weight = 15181.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.0820

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= 0.174
  Angle     :  0.565   6.569   8499  Z= 0.315
  Chirality :  0.038   0.137    956
  Planarity :  0.004   0.051    916
  Dihedral  : 22.301  59.962   1234
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  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: -0.70 (0.90), residues: 41
  loop : -1.18 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 465 
 HIS   0.003   0.001   HIS A 734 
 PHE   0.012   0.002   PHE A 762 
 TYR   0.008   0.001   TYR A 801 
 ARG   0.004   0.000   ARG A 835 

*********************** 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
  32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.8965 (mt) cc_final: 0.8603 (mt)
REVERT: A  559 LEU cc_start: 0.8963 (mt) cc_final: 0.8738 (mt)
REVERT: A  798 VAL cc_start: 0.9436 (t) cc_final: 0.8833 (t)
REVERT: A  802 MET cc_start: 0.9160 (mpp) cc_final: 0.8922 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1231
  time to fit residues: 6.3470
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  : 0.597 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 5 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    1.1144

-------------------------------------------------------------------------------
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 = 0.3251 r_free = 0.3251 target = 0.054884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.043846 restraints weight = 38599.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.045090 restraints weight = 22006.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.045908 restraints weight = 15194.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6111  Z= 0.180
  Angle     :  0.567   6.689   8499  Z= 0.312
  Chirality :  0.038   0.168    956
  Planarity :  0.004   0.046    916
  Dihedral  : 22.204  59.809   1234
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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:  0.21 (0.36), residues: 602
  helix:  1.13 (0.30), residues: 330
  sheet: -0.56 (0.89), residues: 41
  loop : -1.15 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 465 
 HIS   0.007   0.001   HIS A 928 
 PHE   0.008   0.001   PHE A 373 
 TYR   0.008   0.001   TYR A 630 
 ARG   0.004   0.000   ARG A 631 

*********************** 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
  31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 LEU cc_start: 0.9032 (mt) cc_final: 0.8646 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1372
  time to fit residues: 6.9193
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  : 0.615 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    0.4980
   chunk 2 optimal weight:   10.0000
   overall best weight:    2.6584

-------------------------------------------------------------------------------
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**
A 845 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.051850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.041098 restraints weight = 39949.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.042332 restraints weight = 22135.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.043128 restraints weight = 14978.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6111  Z= 0.267
  Angle     :  0.617   6.626   8499  Z= 0.342
  Chirality :  0.040   0.162    956
  Planarity :  0.005   0.049    916
  Dihedral  : 22.293  61.587   1234
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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:  0.81 (0.29), residues: 332
  sheet: -0.64 (0.85), residues: 41
  loop : -1.23 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 465 
 HIS   0.005   0.002   HIS A 327 
 PHE   0.011   0.002   PHE A 771 
 TYR   0.014   0.002   TYR A 659 
 ARG   0.003   0.001   ARG A 873 

*********************** 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  : 0.591 
Fit side-chains
REVERT: A  559 LEU cc_start: 0.9160 (mt) cc_final: 0.8959 (mt)
REVERT: A  798 VAL cc_start: 0.9462 (t) cc_final: 0.8981 (p)
REVERT: A  802 MET cc_start: 0.9237 (mpp) cc_final: 0.8916 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1707
  time to fit residues: 8.4880
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  : 0.842 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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**
A 845 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.050960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.040081 restraints weight = 39609.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.041256 restraints weight = 22448.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.042030 restraints weight = 15443.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2789

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= 0.233
  Angle     :  0.601   6.954   8499  Z= 0.332
  Chirality :  0.040   0.156    956
  Planarity :  0.004   0.040    916
  Dihedral  : 22.390  65.875   1234
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.35 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.35), residues: 602
  helix:  0.76 (0.29), residues: 334
  sheet: -0.29 (0.87), residues: 41
  loop : -1.33 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 465 
 HIS   0.004   0.001   HIS A 327 
 PHE   0.009   0.002   PHE A 771 
 TYR   0.010   0.002   TYR A 787 
 ARG   0.002   0.000   ARG A 835 

*********************** 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
  29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9418 (t) cc_final: 0.8947 (t)
REVERT: A  802 MET cc_start: 0.9174 (mpp) cc_final: 0.8850 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1251
  time to fit residues: 5.8131
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  : 0.567 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 12 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0070
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.4804

-------------------------------------------------------------------------------
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 = 0.3162 r_free = 0.3162 target = 0.051246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.040784 restraints weight = 39669.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.041988 restraints weight = 22157.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.042796 restraints weight = 14990.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6111  Z= 0.186
  Angle     :  0.571   6.180   8499  Z= 0.316
  Chirality :  0.039   0.167    956
  Planarity :  0.004   0.042    916
  Dihedral  : 22.336  68.474   1234
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  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:  0.13 (0.35), residues: 602
  helix:  1.03 (0.29), residues: 331
  sheet: -0.17 (0.85), residues: 41
  loop : -1.24 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.007   0.001   PHE A 771 
 TYR   0.009   0.001   TYR A 497 
 ARG   0.002   0.000   ARG A 835 

*********************** 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
  27 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A  713 ILE cc_start: 0.9132 (mm) cc_final: 0.8867 (mt)
REVERT: A  798 VAL cc_start: 0.9460 (t) cc_final: 0.9060 (p)
REVERT: A  802 MET cc_start: 0.9293 (mpp) cc_final: 0.8957 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1200
  time to fit residues: 5.3454
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  : 0.594 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0070
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.3187 r_free = 0.3187 target = 0.052143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.041661 restraints weight = 39414.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.042875 restraints weight = 21698.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043695 restraints weight = 14637.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3169

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= 0.160
  Angle     :  0.581   6.867   8499  Z= 0.315
  Chirality :  0.039   0.168    956
  Planarity :  0.004   0.079    916
  Dihedral  : 22.247  68.942   1234
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.35), residues: 602
  helix:  1.14 (0.29), residues: 335
  sheet: -0.15 (0.85), residues: 41
  loop : -1.03 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 881 
 PHE   0.011   0.001   PHE A 727 
 TYR   0.009   0.001   TYR A 497 
 ARG   0.002   0.000   ARG A 835 

*********************** 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
  32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A  713 ILE cc_start: 0.9099 (mm) cc_final: 0.8852 (mt)
REVERT: A  798 VAL cc_start: 0.9474 (t) cc_final: 0.9041 (p)
REVERT: A  802 MET cc_start: 0.9296 (mpp) cc_final: 0.8984 (mpp)
REVERT: A  887 GLU cc_start: 0.7928 (tp30) cc_final: 0.7652 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1288
  time to fit residues: 6.6105
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  : 0.631 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3163 r_free = 0.3163 target = 0.051178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.040450 restraints weight = 40020.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.041633 restraints weight = 22621.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.042373 restraints weight = 15548.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6111  Z= 0.181
  Angle     :  0.577   6.434   8499  Z= 0.315
  Chirality :  0.039   0.165    956
  Planarity :  0.004   0.066    916
  Dihedral  : 22.207  69.943   1234
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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:  0.27 (0.36), residues: 602
  helix:  1.11 (0.29), residues: 335
  sheet: -0.02 (0.83), residues: 41
  loop : -1.17 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 866 
 HIS   0.002   0.001   HIS A 509 
 PHE   0.007   0.001   PHE A 771 
 TYR   0.011   0.001   TYR A 795 
 ARG   0.002   0.000   ARG A 835 

*********************** 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
  31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9426 (t) cc_final: 0.9091 (p)
REVERT: A  802 MET cc_start: 0.9191 (mpp) cc_final: 0.8841 (mpp)
REVERT: A  845 ASN cc_start: 0.8783 (t0) cc_final: 0.8421 (m-40)
REVERT: A  887 GLU cc_start: 0.7955 (tp30) cc_final: 0.7686 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1245
  time to fit residues: 6.2434
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  : 0.594 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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 = 0.3119 r_free = 0.3119 target = 0.049478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.038748 restraints weight = 40717.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.039867 restraints weight = 23254.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.040629 restraints weight = 16181.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6111  Z= 0.254
  Angle     :  0.615   6.638   8499  Z= 0.340
  Chirality :  0.040   0.171    956
  Planarity :  0.004   0.058    916
  Dihedral  : 22.320  73.076   1234
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  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: -0.02 (0.35), residues: 602
  helix:  0.88 (0.29), residues: 334
  sheet: -0.07 (0.83), residues: 41
  loop : -1.32 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 866 
 HIS   0.003   0.001   HIS A 327 
 PHE   0.010   0.002   PHE A 771 
 TYR   0.017   0.002   TYR A 787 
 ARG   0.008   0.001   ARG A 562 

*********************** 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
  25 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9437 (t) cc_final: 0.8931 (t)
REVERT: A  802 MET cc_start: 0.9216 (mpp) cc_final: 0.8878 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1569
  time to fit residues: 6.5159
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  : 0.660 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 54 optimal weight:    0.0060
   chunk 15 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0870
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8256

-------------------------------------------------------------------------------
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 = 0.3151 r_free = 0.3151 target = 0.050471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.039879 restraints weight = 39736.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.041033 restraints weight = 22367.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.041808 restraints weight = 15348.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6111  Z= 0.167
  Angle     :  0.583   7.333   8499  Z= 0.321
  Chirality :  0.039   0.142    956
  Planarity :  0.004   0.052    916
  Dihedral  : 22.260  73.292   1234
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    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:  0.13 (0.35), residues: 602
  helix:  0.97 (0.29), residues: 335
  sheet:  0.00 (0.84), residues: 41
  loop : -1.21 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.006   0.001   PHE A 771 
 TYR   0.013   0.001   TYR A 787 
 ARG   0.002   0.000   ARG A 539 

********************** 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
  29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9422 (t) cc_final: 0.9006 (t)
REVERT: A  802 MET cc_start: 0.9348 (mpp) cc_final: 0.8971 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1583
  time to fit residues: 6.8726
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  : 0.652 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 926 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 = 0.3088 r_free = 0.3088 target = 0.047999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.037862 restraints weight = 40952.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.038979 restraints weight = 22794.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.039745 restraints weight = 15524.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6111  Z= 0.337
  Angle     :  0.677   6.995   8499  Z= 0.375
  Chirality :  0.042   0.158    956
  Planarity :  0.005   0.051    916
  Dihedral  : 22.415  76.586   1234
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    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: -0.38 (0.34), residues: 602
  helix:  0.49 (0.28), residues: 335
  sheet:  0.11 (0.85), residues: 41
  loop : -1.38 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 866 
 HIS   0.005   0.001   HIS A 327 
 PHE   0.018   0.002   PHE A 886 
 TYR   0.016   0.002   TYR A 431 
 ARG   0.003   0.000   ARG A 835 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1697.96 seconds
wall clock time: 31 minutes 41.74 seconds (1901.74 seconds total)