Starting phenix.real_space_refine
on Fri Oct 10 13:16:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oo6_17005/10_2025/8oo6_17005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oo6_17005/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oo6_17005/10_2025/8oo6_17005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oo6_17005/10_2025/8oo6_17005.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/10_2025/8oo6_17005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oo6_17005/10_2025/8oo6_17005.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.26
  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: 0.53
  Conformation dependent library (CDL) restraints added in 358.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.82
  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: 1.18

  Time building geometry restraints manager: 0.71 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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.390
  Find NCS groups from input model:        0.030
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (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
 ARG   0.003   0.000   ARG A 781 
 TYR   0.012   0.001   TYR A 801 
 PHE   0.022   0.001   PHE A 762 
 TRP   0.034   0.003   TRP A 465 
 HIS   0.003   0.001   HIS A 734 

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

*********************** 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  : 0.220 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.9011 (mt) cc_final: 0.8642 (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: 0.0525
  time to fit residues: 2.9050
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  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 761 ASN
A 845 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.052645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.041895 restraints weight = 39536.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.043163 restraints weight = 22036.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.043931 restraints weight = 14946.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.044549 restraints weight = 11684.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.044764 restraints weight = 9803.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6111  Z= 0.196
  Angle     :  0.618   6.722   8499  Z= 0.346
  Chirality :  0.040   0.141    956
  Planarity :  0.005   0.052    916
  Dihedral  : 22.365  59.808   1234
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.35), residues: 602
  helix:  0.86 (0.29), residues: 331
  sheet: -0.71 (0.90), residues: 41
  loop : -1.33 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 835 
 TYR   0.010   0.002   TYR A 431 
 PHE   0.013   0.002   PHE A 771 
 TRP   0.023   0.002   TRP A 465 
 HIS   0.006   0.002   HIS A 901 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 6111)
  covalent geometry    : angle       0.61782 ( 8499)
  hydrogen bonds       : bond        0.05002 (  331)
  hydrogen bonds       : angle       4.84152 (  911)

*********************** 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
  28 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  559 LEU cc_start: 0.9107 (mt) cc_final: 0.8891 (mt)
REVERT: A  798 VAL cc_start: 0.9400 (t) cc_final: 0.8742 (t)
REVERT: A  802 MET cc_start: 0.9182 (mpp) cc_final: 0.8901 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0513
  time to fit residues: 2.2827
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  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 528 ASN
A 845 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.053447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.042819 restraints weight = 38794.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.044089 restraints weight = 21602.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.044934 restraints weight = 14555.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045444 restraints weight = 11204.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.045672 restraints weight = 9524.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1725

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= 0.136
  Angle     :  0.579   6.741   8499  Z= 0.318
  Chirality :  0.039   0.157    956
  Planarity :  0.004   0.047    916
  Dihedral  : 22.352  59.897   1234
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.35), residues: 602
  helix:  0.99 (0.29), residues: 330
  sheet: -0.69 (0.87), residues: 41
  loop : -1.24 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 631 
 TYR   0.009   0.001   TYR A 497 
 PHE   0.007   0.001   PHE A 771 
 TRP   0.009   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6111)
  covalent geometry    : angle       0.57866 ( 8499)
  hydrogen bonds       : bond        0.04066 (  331)
  hydrogen bonds       : angle       4.52498 (  911)

*********************** 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
  32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0542
  time to fit residues: 2.8009
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  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0570
   chunk 57 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0060
   overall best weight:    1.0120

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.053545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.042876 restraints weight = 39078.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.044121 restraints weight = 21795.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.044936 restraints weight = 14823.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.045385 restraints weight = 11510.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.045775 restraints weight = 9959.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2034

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= 0.131
  Angle     :  0.573   6.501   8499  Z= 0.315
  Chirality :  0.038   0.160    956
  Planarity :  0.004   0.045    916
  Dihedral  : 22.270  61.630   1234
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.35), residues: 602
  helix:  1.01 (0.29), residues: 330
  sheet: -0.64 (0.85), residues: 41
  loop : -1.13 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.008   0.001   TYR A 497 
 PHE   0.007   0.001   PHE A 771 
 TRP   0.006   0.001   TRP A 513 
 HIS   0.002   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6111)
  covalent geometry    : angle       0.57276 ( 8499)
  hydrogen bonds       : bond        0.03889 (  331)
  hydrogen bonds       : angle       4.42215 (  911)

*********************** 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
  33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9403 (t) cc_final: 0.8915 (t)
REVERT: A  802 MET cc_start: 0.9243 (mpp) cc_final: 0.9027 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0492
  time to fit residues: 2.5825
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  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.051731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.041141 restraints weight = 39866.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.042344 restraints weight = 22084.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.043129 restraints weight = 14950.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.043707 restraints weight = 11626.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.043912 restraints weight = 9810.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6111  Z= 0.183
  Angle     :  0.615   8.619   8499  Z= 0.336
  Chirality :  0.040   0.166    956
  Planarity :  0.004   0.040    916
  Dihedral  : 22.286  65.260   1234
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.35), residues: 602
  helix:  0.87 (0.29), residues: 332
  sheet: -0.75 (0.81), residues: 41
  loop : -1.23 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 873 
 TYR   0.012   0.002   TYR A 659 
 PHE   0.010   0.001   PHE A 771 
 TRP   0.009   0.001   TRP A 513 
 HIS   0.003   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6111)
  covalent geometry    : angle       0.61509 ( 8499)
  hydrogen bonds       : bond        0.04500 (  331)
  hydrogen bonds       : angle       4.51936 (  911)

*********************** 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
  32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9366 (t) cc_final: 0.8922 (t)
REVERT: A  802 MET cc_start: 0.9226 (mpp) cc_final: 0.8884 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0497
  time to fit residues: 2.5905
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  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3189 r_free = 0.3189 target = 0.052356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.041957 restraints weight = 39237.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.043196 restraints weight = 21461.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.044038 restraints weight = 14399.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.044465 restraints weight = 11035.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.044858 restraints weight = 9507.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2793

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= 0.131
  Angle     :  0.574   6.239   8499  Z= 0.315
  Chirality :  0.039   0.133    956
  Planarity :  0.004   0.039    916
  Dihedral  : 22.282  66.892   1234
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.35), residues: 602
  helix:  1.02 (0.29), residues: 332
  sheet: -0.49 (0.83), residues: 41
  loop : -1.18 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.009   0.001   TYR A 497 
 PHE   0.006   0.001   PHE A 771 
 TRP   0.004   0.001   TRP A 866 
 HIS   0.004   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6111)
  covalent geometry    : angle       0.57430 ( 8499)
  hydrogen bonds       : bond        0.03877 (  331)
  hydrogen bonds       : angle       4.36256 (  911)

*********************** 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
  30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  512 MET cc_start: 0.8680 (ttp) cc_final: 0.8390 (ttp)
REVERT: A  713 ILE cc_start: 0.9064 (mm) cc_final: 0.8802 (mt)
REVERT: A  798 VAL cc_start: 0.9365 (t) cc_final: 0.8939 (t)
REVERT: A  802 MET cc_start: 0.9333 (mpp) cc_final: 0.9042 (mpp)
REVERT: A  887 GLU cc_start: 0.7990 (tp30) cc_final: 0.7678 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0554
  time to fit residues: 2.5926
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  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.3121 r_free = 0.3121 target = 0.049598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.038842 restraints weight = 40982.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.040030 restraints weight = 22909.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.040753 restraints weight = 15631.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.041292 restraints weight = 12384.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.041562 restraints weight = 10566.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6111  Z= 0.220
  Angle     :  0.645   7.195   8499  Z= 0.356
  Chirality :  0.041   0.142    956
  Planarity :  0.005   0.080    916
  Dihedral  : 22.357  70.316   1234
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.34), residues: 602
  helix:  0.71 (0.28), residues: 336
  sheet: -0.41 (0.83), residues: 41
  loop : -1.34 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 631 
 TYR   0.012   0.002   TYR A 431 
 PHE   0.012   0.002   PHE A 771 
 TRP   0.008   0.001   TRP A 866 
 HIS   0.004   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 6111)
  covalent geometry    : angle       0.64530 ( 8499)
  hydrogen bonds       : bond        0.05291 (  331)
  hydrogen bonds       : angle       4.66417 (  911)

*********************** 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
  29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  512 MET cc_start: 0.8861 (ttp) cc_final: 0.8643 (ttp)
REVERT: A  798 VAL cc_start: 0.9338 (t) cc_final: 0.8966 (t)
REVERT: A  802 MET cc_start: 0.9302 (mpp) cc_final: 0.8934 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0543
  time to fit residues: 2.5872
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  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3163 r_free = 0.3163 target = 0.051160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.040281 restraints weight = 40613.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041467 restraints weight = 22742.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.042251 restraints weight = 15615.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.042711 restraints weight = 12273.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.043052 restraints weight = 10646.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3435

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= 0.128
  Angle     :  0.589   6.400   8499  Z= 0.319
  Chirality :  0.039   0.164    956
  Planarity :  0.004   0.067    916
  Dihedral  : 22.328  70.555   1234
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.18 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.35), residues: 602
  helix:  1.01 (0.29), residues: 334
  sheet: -0.26 (0.84), residues: 41
  loop : -1.25 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 875 
 TYR   0.009   0.001   TYR A 497 
 PHE   0.007   0.001   PHE A 727 
 TRP   0.007   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6111)
  covalent geometry    : angle       0.58855 ( 8499)
  hydrogen bonds       : bond        0.03928 (  331)
  hydrogen bonds       : angle       4.32397 (  911)

*********************** 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
  29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9343 (t) cc_final: 0.8897 (t)
REVERT: A  802 MET cc_start: 0.9333 (mpp) cc_final: 0.8961 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0504
  time to fit residues: 2.4015
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  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 54 optimal weight:    0.2980
   chunk 11 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3169 r_free = 0.3169 target = 0.051310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.040940 restraints weight = 40567.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.042134 restraints weight = 22560.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.042772 restraints weight = 15267.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.043386 restraints weight = 12186.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.043671 restraints weight = 10206.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3583

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= 0.129
  Angle     :  0.571   6.878   8499  Z= 0.313
  Chirality :  0.039   0.132    956
  Planarity :  0.004   0.059    916
  Dihedral  : 22.256  71.525   1234
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.35), residues: 602
  helix:  0.99 (0.29), residues: 336
  sheet: -0.18 (0.84), residues: 41
  loop : -1.21 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.008   0.001   TYR A 706 
 PHE   0.007   0.001   PHE A 771 
 TRP   0.017   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6111)
  covalent geometry    : angle       0.57086 ( 8499)
  hydrogen bonds       : bond        0.03860 (  331)
  hydrogen bonds       : angle       4.31081 (  911)

*********************** 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
  30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9429 (t) cc_final: 0.8891 (t)
REVERT: A  802 MET cc_start: 0.9362 (mpp) cc_final: 0.9009 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0667
  time to fit residues: 2.9734
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  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0870
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.9560

-------------------------------------------------------------------------------
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 = 0.3165 r_free = 0.3165 target = 0.051069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.040356 restraints weight = 39643.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.041546 restraints weight = 22271.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.042300 restraints weight = 15196.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.042823 restraints weight = 11927.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.043065 restraints weight = 10140.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3753

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= 0.126
  Angle     :  0.573   6.304   8499  Z= 0.313
  Chirality :  0.039   0.134    956
  Planarity :  0.004   0.052    916
  Dihedral  : 22.180  71.862   1234
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.35), residues: 602
  helix:  1.04 (0.29), residues: 336
  sheet:  0.10 (0.86), residues: 41
  loop : -1.22 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.014   0.001   TYR A 706 
 PHE   0.006   0.001   PHE A 771 
 TRP   0.008   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6111)
  covalent geometry    : angle       0.57255 ( 8499)
  hydrogen bonds       : bond        0.03705 (  331)
  hydrogen bonds       : angle       4.23210 (  911)

********************** 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
  31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  798 VAL cc_start: 0.9374 (t) cc_final: 0.8950 (t)
REVERT: A  802 MET cc_start: 0.9368 (mpp) cc_final: 0.9005 (mpp)
REVERT: A  845 ASN cc_start: 0.8723 (t0) cc_final: 0.8509 (t0)
REVERT: A  878 MET cc_start: 0.8745 (tpp) cc_final: 0.8410 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0491
  time to fit residues: 2.4862
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  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0770
   chunk 25 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.5944

-------------------------------------------------------------------------------
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 = 0.3146 r_free = 0.3146 target = 0.050208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.039970 restraints weight = 40112.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.041133 restraints weight = 22517.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.041916 restraints weight = 15354.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.042308 restraints weight = 11864.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.042672 restraints weight = 10266.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6111  Z= 0.143
  Angle     :  0.578   7.140   8499  Z= 0.317
  Chirality :  0.039   0.144    956
  Planarity :  0.004   0.049    916
  Dihedral  : 22.180  73.224   1234
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.35), residues: 602
  helix:  0.99 (0.29), residues: 335
  sheet:  0.28 (0.86), residues: 41
  loop : -1.25 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.017   0.002   TYR A 787 
 PHE   0.008   0.001   PHE A 771 
 TRP   0.007   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6111)
  covalent geometry    : angle       0.57783 ( 8499)
  hydrogen bonds       : bond        0.04056 (  331)
  hydrogen bonds       : angle       4.32615 (  911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 948.69 seconds
wall clock time: 17 minutes 6.14 seconds (1026.14 seconds total)