Starting phenix.real_space_refine
on Tue Mar  3 15:18:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nxf_12638/03_2026/7nxf_12638.cif"
  }
  resolution = 3.1
  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: 7
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      23      5.16       5
     C    4130      2.51       5
     N    1060      2.21       5
     O    1188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6405
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 829, 6376
          Classifications: {'peptide': 829}
          Link IDs: {'PTRANS': 31, 'TRANS': 797}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {'  K': 1, ' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.28, per 1000 atoms: 0.20
  Number of scatterers: 6405
  At special positions: 0
  Unit cell: (92.07, 72.819, 125.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       1     19.00
     S      23     16.00
     P       2     15.00
     Mg      1     11.99
     O    1188      8.00
     N    1060      7.00
     C    4130      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: 0.49
  Conformation dependent library (CDL) restraints added in 199.4 milliseconds
  

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1514

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      52.8% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.754A  pdb=" N   THR A  82 " --> pdb=" O   MET A  79 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASP A  83 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 79 through 83'
    Processing helix  chain 'A' and resid 113 through 119
      removed outlier: 3.602A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
    Processing helix  chain 'A' and resid 142 through 175
      removed outlier: 3.857A  pdb=" N   ASP A 170 " --> pdb=" O   GLY A 166 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 315
    Processing helix  chain 'A' and resid 318 through 334
      removed outlier: 3.619A  pdb=" N   VAL A 334 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 356
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 402 through 411
      removed outlier: 4.379A  pdb=" N   LEU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 411 " --> pdb=" O   THR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 429
      removed outlier: 3.792A  pdb=" N   LYS A 424 " --> pdb=" O   ASP A 420 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A 427 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 485
      removed outlier: 3.635A  pdb=" N   LEU A 481 " --> pdb=" O   PRO A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 508
      removed outlier: 3.518A  pdb=" N   GLN A 496 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ALA A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 550
      removed outlier: 3.850A  pdb=" N   THR A 549 " --> pdb=" O   CYS A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 573
    Processing helix  chain 'A' and resid 581 through 585
    Processing helix  chain 'A' and resid 593 through 603
      removed outlier: 3.822A  pdb=" N   ASP A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 625
      removed outlier: 3.519A  pdb=" N   LYS A 615 " --> pdb=" O   PHE A 611 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 616 " --> pdb=" O   PRO A 612 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG A 625 " --> pdb=" O   ILE A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 645
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 670 through 714
      removed outlier: 3.967A  pdb=" N   ILE A 674 " --> pdb=" O   GLY A 670 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A 708 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 729
    Processing helix  chain 'A' and resid 751 through 781
      removed outlier: 3.686A  pdb=" N   MET A 777 " --> pdb=" O   THR A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 807
    Processing helix  chain 'A' and resid 808 through 813
    Processing helix  chain 'A' and resid 824 through 845
    Processing helix  chain 'A' and resid 853 through 878
      removed outlier: 3.661A  pdb=" N   VAL A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 919
    Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205
      removed outlier: 3.632A  pdb=" N   VAL A 204 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA A 256 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226
      removed outlier: 6.518A  pdb=" N   GLN A 224 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA A 250 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 360
      removed outlier: 6.833A  pdb=" N   VAL A 629 " --> pdb=" O   THR A 647 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ILE A 649 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   MET A 631 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 630 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   THR A 632 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   CYS A 376 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LEU A 375 " --> pdb=" O   LYS A 555 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   LEU A 557 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   SER A 377 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   TYR A 579 " --> pdb=" O   ALA A 608 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 390
      removed outlier: 6.401A  pdb=" N   ILE A 526 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   ARG A 517 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLY A 528 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   GLU A 463 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   VAL A 445 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)

    341 hydrogen bonds defined for protein.
    1011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1504
        1.33 -     1.45: 1404
        1.45 -     1.58: 3585
        1.58 -     1.70: 0
        1.70 -     1.83: 40
  Bond restraints: 6533
  Sorted by residual:
  bond pdb=" O5' ADP A1001 "
       pdb=" PA  ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.610  1.826 -0.216 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" O3A ADP A1001 "
       pdb=" PB  ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.610  1.808 -0.198 2.00e-02 2.50e+03 9.77e+01
  bond pdb=" C5  ADP A1001 "
       pdb=" C6  ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.490  1.401  0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" C8  ADP A1001 "
       pdb=" N9  ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.337  1.409 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C5' ADP A1001 "
       pdb=" O5' ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.426  1.354  0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 6528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.96: 8832
        3.96 -     7.92: 33
        7.92 -    11.88: 5
       11.88 -    15.84: 5
       15.84 -    19.80: 1
  Bond angle restraints: 8876
  Sorted by residual:
  angle pdb=" O1A ADP A1001 "
        pdb=" PA  ADP A1001 "
        pdb=" O5' ADP A1001 "
      ideal   model   delta    sigma   weight residual
     108.20   88.40   19.80 3.00e+00 1.11e-01 4.36e+01
  angle pdb=" O2A ADP A1001 "
        pdb=" PA  ADP A1001 "
        pdb=" O3A ADP A1001 "
      ideal   model   delta    sigma   weight residual
     108.20  123.77  -15.57 3.00e+00 1.11e-01 2.69e+01
  angle pdb=" C5' ADP A1001 "
        pdb=" O5' ADP A1001 "
        pdb=" PA  ADP A1001 "
      ideal   model   delta    sigma   weight residual
     120.50  105.39   15.11 3.00e+00 1.11e-01 2.54e+01
  angle pdb=" PA  ADP A1001 "
        pdb=" O3A ADP A1001 "
        pdb=" PB  ADP A1001 "
      ideal   model   delta    sigma   weight residual
     120.50  106.19   14.31 3.00e+00 1.11e-01 2.28e+01
  angle pdb=" O3A ADP A1001 "
        pdb=" PB  ADP A1001 "
        pdb=" O3B ADP A1001 "
      ideal   model   delta    sigma   weight residual
     108.20   94.68   13.52 3.00e+00 1.11e-01 2.03e+01
  ... (remaining 8871 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.30: 3744
       30.30 -    60.60: 109
       60.60 -    90.90: 4
       90.90 -   121.20: 0
      121.20 -   151.50: 2
  Dihedral angle restraints: 3859
    sinusoidal: 1498
      harmonic: 2361
  Sorted by residual:
  dihedral pdb=" O2A ADP A1001 "
           pdb=" O3A ADP A1001 "
           pdb=" PA  ADP A1001 "
           pdb=" PB  ADP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   91.50 -151.50     1      2.00e+01 2.50e-03 4.51e+01
  dihedral pdb=" O1B ADP A1001 "
           pdb=" O3A ADP A1001 "
           pdb=" PB  ADP A1001 "
           pdb=" PA  ADP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   74.18 -134.18     1      2.00e+01 2.50e-03 4.07e+01
  dihedral pdb=" CA  VAL A  93 "
           pdb=" C   VAL A  93 "
           pdb=" N   VAL A  94 "
           pdb=" CA  VAL A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.08  -28.92     0      5.00e+00 4.00e-02 3.34e+01
  ... (remaining 3856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 685
       0.038 -    0.076: 264
       0.076 -    0.114: 73
       0.114 -    0.152: 13
       0.152 -    0.190: 4
  Chirality restraints: 1039
  Sorted by residual:
  chirality pdb=" C2' ADP A1001 "
            pdb=" C1' ADP A1001 "
            pdb=" C3' ADP A1001 "
            pdb=" O2' ADP A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.70    0.19 2.00e-01 2.50e+01 9.02e-01
  chirality pdb=" CB  THR A 267 "
            pdb=" CA  THR A 267 "
            pdb=" OG1 THR A 267 "
            pdb=" CG2 THR A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.31e-01
  chirality pdb=" CG  LEU A 702 "
            pdb=" CB  LEU A 702 "
            pdb=" CD1 LEU A 702 "
            pdb=" CD2 LEU A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.02e-01
  ... (remaining 1036 not shown)

  Planarity restraints: 1118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 709 "    0.030 2.00e-02 2.50e+03   2.35e-02 1.38e+01
        pdb=" CG  TRP A 709 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 709 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 709 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 709 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 709 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 709 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 709 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 709 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 709 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 592 "   -0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO A 593 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 846 "   -0.023 2.00e-02 2.50e+03   1.89e-02 8.94e+00
        pdb=" CG  TRP A 846 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 846 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 846 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 846 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 846 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 846 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 846 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 846 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 846 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1115 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 2206
        2.85 -     3.42: 7232
        3.42 -     4.00: 11393
        4.00 -     4.57: 16530
        4.57 -     5.14: 23451
  Nonbonded interactions: 60812
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 246 "
            pdb=" OG  SER A 249 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   THR A 773 "
            pdb=" OG1 THR A 776 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OE2 GLU A 602 "
            pdb=" OH  TYR A 627 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O4' ADP A1001 "
            pdb=" O5' ADP A1001 "
     model   vdw
     2.391 2.432
  nonbonded pdb=" OD2 ASP A 403 "
            pdb=" OG1 THR A 407 "
     model   vdw
     2.394 3.040
  ... (remaining 60807 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.620
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
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      :  0.006   0.216   6533  Z= 0.291
  Angle     :  0.816  19.804   8876  Z= 0.391
  Chirality :  0.044   0.190   1039
  Planarity :  0.005   0.082   1118
  Dihedral  : 14.198 151.503   2345
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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 are not related in a simple way.
  whole: -0.71 (0.29), residues: 823
  helix:  0.88 (0.25), residues: 424
  sheet: -1.48 (0.68), residues: 53
  loop : -2.07 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 859 
 TYR   0.016   0.002   TYR A 691 
 PHE   0.012   0.001   PHE A 841 
 TRP   0.063   0.003   TRP A 709 
 HIS   0.006   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 6533)
  covalent geometry    : angle       0.81582 ( 8876)
  hydrogen bonds       : bond        0.17217 (  341)
  hydrogen bonds       : angle       6.19490 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7979 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1197
  time to fit residues: 11.6202
Evaluate side-chains
  44 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.094575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.065065 restraints weight = 18812.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.35
r_work: 0.3086 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6533  Z= 0.134
  Angle     :  0.646   7.494   8876  Z= 0.325
  Chirality :  0.042   0.161   1039
  Planarity :  0.004   0.057   1118
  Dihedral  :  8.277 136.713    888
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.33 %
    Favored  : 90.64 %
  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 are not related in a simple way.
  whole: -0.37 (0.30), residues: 823
  helix:  1.42 (0.26), residues: 426
  sheet: -1.51 (0.65), residues: 56
  loop : -2.30 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  96 
 TYR   0.017   0.001   TYR A 691 
 PHE   0.008   0.001   PHE A 868 
 TRP   0.028   0.001   TRP A 709 
 HIS   0.006   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6533)
  covalent geometry    : angle       0.64580 ( 8876)
  hydrogen bonds       : bond        0.04329 (  341)
  hydrogen bonds       : angle       4.68598 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8015 (p90) cc_final: 0.7092 (p90)
REVERT: A  444 LYS cc_start: 0.7587 (mmmt) cc_final: 0.7274 (mmmt)
REVERT: A  469 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8111 (mmm160)
REVERT: A  496 GLN cc_start: 0.8576 (pp30) cc_final: 0.8328 (pm20)
  outliers start: 7
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0810
  time to fit residues: 6.3624
Evaluate side-chains
  53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0060
   chunk 46 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.5602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.091366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.061111 restraints weight = 19086.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 3.33
r_work: 0.3008 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6533  Z= 0.204
  Angle     :  0.651   6.486   8876  Z= 0.328
  Chirality :  0.043   0.139   1039
  Planarity :  0.004   0.057   1118
  Dihedral  :  7.951 130.696    888
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.53 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.30), residues: 823
  helix:  1.60 (0.25), residues: 443
  sheet: -1.91 (0.62), residues: 57
  loop : -2.38 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.016   0.001   TYR A 691 
 PHE   0.011   0.001   PHE A 705 
 TRP   0.025   0.002   TRP A 709 
 HIS   0.006   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6533)
  covalent geometry    : angle       0.65097 ( 8876)
  hydrogen bonds       : bond        0.04099 (  341)
  hydrogen bonds       : angle       4.53193 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8106 (p90) cc_final: 0.7784 (p90)
REVERT: A  444 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7355 (mmmt)
REVERT: A  469 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8046 (mmm160)
  outliers start: 13
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0822
  time to fit residues: 6.0542
Evaluate side-chains
  50 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0970
   chunk 78 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 683 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.093817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.063962 restraints weight = 18854.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.33
r_work: 0.3061 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6533  Z= 0.110
  Angle     :  0.581   6.488   8876  Z= 0.289
  Chirality :  0.041   0.134   1039
  Planarity :  0.004   0.049   1118
  Dihedral  :  7.535 127.479    888
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.28 %
    Favored  : 85.96 %
  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 are not related in a simple way.
  whole:  0.14 (0.30), residues: 823
  helix:  1.92 (0.26), residues: 437
  sheet: -1.73 (0.62), residues: 55
  loop : -2.23 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.015   0.001   TYR A 691 
 PHE   0.009   0.001   PHE A 841 
 TRP   0.012   0.001   TRP A 846 
 HIS   0.006   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6533)
  covalent geometry    : angle       0.58150 ( 8876)
  hydrogen bonds       : bond        0.03355 (  341)
  hydrogen bonds       : angle       4.22823 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.9373 (tt) cc_final: 0.9051 (mm)
REVERT: A  222 PHE cc_start: 0.8111 (p90) cc_final: 0.7838 (p90)
REVERT: A  444 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7524 (mmmt)
REVERT: A  469 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8030 (mmm160)
REVERT: A  496 GLN cc_start: 0.8983 (pp30) cc_final: 0.8757 (pp30)
REVERT: A  533 MET cc_start: 0.8187 (ttt) cc_final: 0.7930 (ppp)
  outliers start: 12
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0726
  time to fit residues: 5.7257
Evaluate side-chains
  56 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 75 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 806 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.091004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.060735 restraints weight = 19271.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 3.32
r_work: 0.2988 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6533  Z= 0.195
  Angle     :  0.615   6.987   8876  Z= 0.307
  Chirality :  0.042   0.135   1039
  Planarity :  0.004   0.046   1118
  Dihedral  :  7.359 122.984    888
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.87 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.30), residues: 823
  helix:  2.07 (0.26), residues: 438
  sheet: -1.93 (0.59), residues: 57
  loop : -2.26 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 517 
 TYR   0.014   0.001   TYR A 691 
 PHE   0.012   0.001   PHE A 705 
 TRP   0.018   0.001   TRP A 846 
 HIS   0.006   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 6533)
  covalent geometry    : angle       0.61523 ( 8876)
  hydrogen bonds       : bond        0.03718 (  341)
  hydrogen bonds       : angle       4.33859 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8167 (p90) cc_final: 0.7853 (p90)
REVERT: A  444 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7549 (mmmt)
REVERT: A  469 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.7989 (mmm160)
REVERT: A  533 MET cc_start: 0.8215 (ttt) cc_final: 0.7992 (ppp)
  outliers start: 15
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0747
  time to fit residues: 5.1218
Evaluate side-chains
  52 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    0.3980
   chunk 72 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.092523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062721 restraints weight = 19041.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 3.35
r_work: 0.3032 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6533  Z= 0.108
  Angle     :  0.569   6.525   8876  Z= 0.281
  Chirality :  0.040   0.133   1039
  Planarity :  0.003   0.045   1118
  Dihedral  :  7.091 120.319    888
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.01 %
    Favored  : 84.50 %
  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 are not related in a simple way.
  whole:  0.33 (0.30), residues: 823
  helix:  2.11 (0.26), residues: 439
  sheet: -1.91 (0.59), residues: 57
  loop : -2.15 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 517 
 TYR   0.015   0.001   TYR A 691 
 PHE   0.008   0.001   PHE A 841 
 TRP   0.012   0.001   TRP A 846 
 HIS   0.004   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6533)
  covalent geometry    : angle       0.56936 ( 8876)
  hydrogen bonds       : bond        0.03271 (  341)
  hydrogen bonds       : angle       4.14220 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8196 (p90) cc_final: 0.7915 (p90)
REVERT: A  444 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7557 (mmmt)
REVERT: A  469 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8006 (mmm160)
REVERT: A  800 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8615 (tm-30)
REVERT: A  805 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8445 (mt-10)
  outliers start: 17
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0817
  time to fit residues: 6.3697
Evaluate side-chains
  56 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 TYR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 49 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.5778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.094743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064343 restraints weight = 19064.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 3.58
r_work: 0.3080 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6533  Z= 0.106
  Angle     :  0.579   9.854   8876  Z= 0.282
  Chirality :  0.040   0.175   1039
  Planarity :  0.003   0.044   1118
  Dihedral  :  6.756 118.686    888
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.33 %
    Favored  : 84.06 %
  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 are not related in a simple way.
  whole:  0.47 (0.31), residues: 823
  helix:  2.26 (0.26), residues: 438
  sheet: -1.88 (0.59), residues: 58
  loop : -2.14 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.013   0.001   TYR A 691 
 PHE   0.007   0.001   PHE A 841 
 TRP   0.009   0.001   TRP A 846 
 HIS   0.010   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6533)
  covalent geometry    : angle       0.57893 ( 8876)
  hydrogen bonds       : bond        0.03150 (  341)
  hydrogen bonds       : angle       4.01988 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8209 (p90) cc_final: 0.7974 (p90)
REVERT: A  444 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7560 (mmmt)
REVERT: A  469 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7963 (mmm160)
REVERT: A  800 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8842 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 57
  average time/residue: 0.0835
  time to fit residues: 6.5335
Evaluate side-chains
  54 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0870
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0270
   chunk 58 optimal weight:    0.0470
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.3716

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.093862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.064376 restraints weight = 18957.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 3.37
r_work: 0.3093 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6533  Z= 0.100
  Angle     :  0.579  11.543   8876  Z= 0.279
  Chirality :  0.040   0.171   1039
  Planarity :  0.003   0.043   1118
  Dihedral  :  6.590 123.694    888
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.91 %
    Favored  : 83.92 %
  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 are not related in a simple way.
  whole:  0.49 (0.30), residues: 823
  helix:  2.28 (0.26), residues: 438
  sheet: -1.92 (0.57), residues: 57
  loop : -2.11 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 570 
 TYR   0.012   0.001   TYR A 691 
 PHE   0.007   0.001   PHE A 841 
 TRP   0.007   0.001   TRP A 844 
 HIS   0.010   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6533)
  covalent geometry    : angle       0.57881 ( 8876)
  hydrogen bonds       : bond        0.02994 (  341)
  hydrogen bonds       : angle       3.94011 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8096 (p90) cc_final: 0.7892 (p90)
REVERT: A  444 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7599 (mmmt)
REVERT: A  469 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8075 (mmm160)
REVERT: A  496 GLN cc_start: 0.9031 (pp30) cc_final: 0.8752 (pp30)
REVERT: A  698 LEU cc_start: 0.9106 (tt) cc_final: 0.8813 (tp)
REVERT: A  800 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8723 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0816
  time to fit residues: 6.5810
Evaluate side-chains
  55 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  701 HIS
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 33 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.091915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.062269 restraints weight = 19439.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 3.43
r_work: 0.3049 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6533  Z= 0.135
  Angle     :  0.589  10.151   8876  Z= 0.283
  Chirality :  0.041   0.192   1039
  Planarity :  0.003   0.044   1118
  Dihedral  :  6.538 127.358    888
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.50 %
    Favored  : 83.04 %
  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 are not related in a simple way.
  whole:  0.51 (0.30), residues: 823
  helix:  2.26 (0.26), residues: 440
  sheet: -1.71 (0.58), residues: 58
  loop : -2.12 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 695 
 TYR   0.011   0.001   TYR A 691 
 PHE   0.009   0.001   PHE A 705 
 TRP   0.011   0.001   TRP A 846 
 HIS   0.011   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6533)
  covalent geometry    : angle       0.58927 ( 8876)
  hydrogen bonds       : bond        0.03219 (  341)
  hydrogen bonds       : angle       4.00861 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8123 (p90) cc_final: 0.7903 (p90)
REVERT: A  444 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7595 (mmmt)
REVERT: A  469 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7985 (mmm160)
  outliers start: 10
  outliers final: 8
  residues processed: 52
  average time/residue: 0.0787
  time to fit residues: 5.6037
Evaluate side-chains
  53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 TYR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  701 HIS
Chi-restraints excluded: chain A residue  805 GLU
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0770
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0070
   chunk 77 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.4358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.093399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063926 restraints weight = 18896.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 3.37
r_work: 0.3093 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6533  Z= 0.101
  Angle     :  0.592  10.290   8876  Z= 0.282
  Chirality :  0.040   0.198   1039
  Planarity :  0.003   0.043   1118
  Dihedral  :  6.416 130.060    888
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 15.94 %
    Favored  : 83.04 %
  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 are not related in a simple way.
  whole:  0.51 (0.30), residues: 823
  helix:  2.27 (0.26), residues: 438
  sheet: -1.80 (0.58), residues: 57
  loop : -2.10 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.012   0.001   TYR A 691 
 PHE   0.008   0.001   PHE A 685 
 TRP   0.007   0.001   TRP A 846 
 HIS   0.011   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6533)
  covalent geometry    : angle       0.59241 ( 8876)
  hydrogen bonds       : bond        0.02984 (  341)
  hydrogen bonds       : angle       3.91283 ( 1011)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7587 (mmmt)
REVERT: A  469 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7994 (mmm160)
REVERT: A  800 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8706 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0894
  time to fit residues: 6.1524
Evaluate side-chains
  52 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 TYR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  701 HIS
Chi-restraints excluded: chain A residue  837 LEU
Chi-restraints excluded: chain A residue  846 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0870
   chunk 17 optimal weight:    0.0980
   chunk 77 optimal weight:    0.0170
   chunk 80 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.094282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.064831 restraints weight = 19120.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 3.42
r_work: 0.3111 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6533  Z= 0.098
  Angle     :  0.575  10.127   8876  Z= 0.275
  Chirality :  0.041   0.216   1039
  Planarity :  0.003   0.044   1118
  Dihedral  :  6.318 132.568    888
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.23 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.30), residues: 823
  helix:  2.30 (0.26), residues: 439
  sheet: -1.73 (0.59), residues: 57
  loop : -2.07 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.010   0.001   TYR A 691 
 PHE   0.006   0.001   PHE A 841 
 TRP   0.006   0.001   TRP A 844 
 HIS   0.010   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6533)
  covalent geometry    : angle       0.57521 ( 8876)
  hydrogen bonds       : bond        0.02883 (  341)
  hydrogen bonds       : angle       3.86828 ( 1011)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1809.60 seconds
wall clock time: 31 minutes 33.33 seconds (1893.33 seconds total)