Starting phenix.real_space_refine
on Sun May 11 06:21:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qa4_18298/05_2025/8qa4_18298_trim.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2448      2.51       5
     N     614      2.21       5
     O     748      1.98       5
     H    3686      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7506
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3685
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 14, 'TRANS': 215}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 42
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 42
          Classifications: {'water': 14}
          Link IDs: {None: 13}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.02, per 1000 atoms: 0.94
  Number of scatterers: 7506
  At special positions: 0
  Unit cell: (106.19, 90.118, 50.512, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     748      8.00
     N     614      7.00
     C    2448      6.00
     H    3686      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 600.6 milliseconds
  

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  872

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      44.6% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 415 through 421
    Processing helix  chain 'A' and resid 427 through 440
      removed outlier: 3.986A  pdb=" N   VAL A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
    Processing helix  chain 'A' and resid 467 through 476
    Processing helix  chain 'A' and resid 518 through 530
      removed outlier: 3.801A  pdb=" N   LYS A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 555
    Processing helix  chain 'A' and resid 576 through 595
      removed outlier: 3.860A  pdb=" N   MET A 581 " --> pdb=" O   PRO A 577 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ASP A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLU A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TRP A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 616
      removed outlier: 3.738A  pdb=" N   TYR A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 644
    Processing helix  chain 'B' and resid 416 through 421
    Processing helix  chain 'B' and resid 427 through 440
      removed outlier: 3.986A  pdb=" N   VAL B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 466
    Processing helix  chain 'B' and resid 467 through 476
    Processing helix  chain 'B' and resid 518 through 530
      removed outlier: 3.802A  pdb=" N   LYS B 530 " --> pdb=" O   LEU B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 555
    Processing helix  chain 'B' and resid 576 through 595
      removed outlier: 3.860A  pdb=" N   MET B 581 " --> pdb=" O   PRO B 577 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE B 582 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ASP B 585 " --> pdb=" O   MET B 581 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLU B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   TRP B 591 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE B 592 " --> pdb=" O   PHE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 603 through 616
      removed outlier: 3.738A  pdb=" N   TYR B 616 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 644
    Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 485
      removed outlier: 5.311A  pdb=" N   THR A 481 " --> pdb=" O   PHE A 516 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   PHE A 516 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA A 511 " --> pdb=" O   ASP A 623 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ASN A 542 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   GLU A 546 " --> pdb=" O   ASN A 542 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 492
      removed outlier: 5.102A  pdb=" N   VAL A 507 " --> pdb=" O   GLY A 490 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ALA A 558 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL A 574 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR A 560 " --> pdb=" O   PRO A 572 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 480 through 485
      removed outlier: 5.311A  pdb=" N   THR B 481 " --> pdb=" O   PHE B 516 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   PHE B 516 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA B 511 " --> pdb=" O   ASP B 623 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ASN B 542 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   GLU B 546 " --> pdb=" O   ASN B 542 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 488 through 492
      removed outlier: 5.102A  pdb=" N   VAL B 507 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ALA B 558 " --> pdb=" O   VAL B 574 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL B 574 " --> pdb=" O   ALA B 558 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR B 560 " --> pdb=" O   PRO B 572 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    471 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: 2.76

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 830
        1.05 -     1.24: 3378
        1.24 -     1.43: 1290
        1.43 -     1.62: 2070
        1.62 -     1.81: 16
  Bond restraints: 7584
  Sorted by residual:
  bond pdb=" CZ2 TRP B 633 "
       pdb=" HZ2 TRP B 633 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" CE2 TYR B 438 "
       pdb=" HE2 TYR B 438 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" N   GLU A 553 "
       pdb=" H   GLU A 553 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" CE1 TYR B 506 "
       pdb=" HE1 TYR B 506 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   ASN B 456 "
       pdb=" H   ASN B 456 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 7579 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 10990
        2.69 -     5.38: 1985
        5.38 -     8.07: 607
        8.07 -    10.76: 40
       10.76 -    13.45: 14
  Bond angle restraints: 13636
  Sorted by residual:
  angle pdb=" C   GLU B 600 "
        pdb=" N   GLU B 601 "
        pdb=" CA  GLU B 601 "
      ideal   model   delta    sigma   weight residual
     120.54  132.31  -11.77 1.35e+00 5.49e-01 7.60e+01
  angle pdb=" C   GLU A 600 "
        pdb=" N   GLU A 601 "
        pdb=" CA  GLU A 601 "
      ideal   model   delta    sigma   weight residual
     120.54  132.29  -11.75 1.35e+00 5.49e-01 7.58e+01
  angle pdb=" CA  SAH A 701 "
        pdb=" C   SAH A 701 "
        pdb=" O   SAH A 701 "
      ideal   model   delta    sigma   weight residual
     120.80  107.35   13.45 1.70e+00 3.46e-01 6.26e+01
  angle pdb=" CA  SAH B 701 "
        pdb=" C   SAH B 701 "
        pdb=" O   SAH B 701 "
      ideal   model   delta    sigma   weight residual
     120.80  107.39   13.41 1.70e+00 3.46e-01 6.23e+01
  angle pdb=" CA  ASP B 495 "
        pdb=" CB  ASP B 495 "
        pdb=" CG  ASP B 495 "
      ideal   model   delta    sigma   weight residual
     112.60  120.22   -7.62 1.00e+00 1.00e+00 5.80e+01
  ... (remaining 13631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3192
       18.00 -    35.99: 192
       35.99 -    53.99: 91
       53.99 -    71.99: 49
       71.99 -    89.99: 10
  Dihedral angle restraints: 3534
    sinusoidal: 1900
      harmonic: 1634
  Sorted by residual:
  dihedral pdb=" C   GLU B 602 "
           pdb=" N   GLU B 602 "
           pdb=" CA  GLU B 602 "
           pdb=" CB  GLU B 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.60   12.00     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" C   GLU A 602 "
           pdb=" N   GLU A 602 "
           pdb=" CA  GLU A 602 "
           pdb=" CB  GLU A 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.58   11.98     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" N   GLU B 602 "
           pdb=" C   GLU B 602 "
           pdb=" CA  GLU B 602 "
           pdb=" CB  GLU B 602 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.63  -11.83     0      2.50e+00 1.60e-01 2.24e+01
  ... (remaining 3531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 448
       0.142 -    0.284: 70
       0.284 -    0.426: 10
       0.426 -    0.568: 37
       0.568 -    0.710: 19
  Chirality restraints: 584
  Sorted by residual:
  chirality pdb=" CG  LEU A 472 "
            pdb=" CB  LEU A 472 "
            pdb=" CD1 LEU A 472 "
            pdb=" CD2 LEU A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.88   -0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" CG  LEU B 472 "
            pdb=" CB  LEU B 472 "
            pdb=" CD1 LEU B 472 "
            pdb=" CD2 LEU B 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.88   -0.71 2.00e-01 2.50e+01 1.25e+01
  chirality pdb=" CB  ILE A 608 "
            pdb=" CA  ILE A 608 "
            pdb=" CG1 ILE A 608 "
            pdb=" CG2 ILE A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.97    0.68 2.00e-01 2.50e+01 1.14e+01
  ... (remaining 581 not shown)

  Planarity restraints: 1114
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 644 "    0.161 2.00e-02 2.50e+03   4.80e-01 3.45e+03
        pdb=" CG  ASN B 644 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 644 "   -0.158 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 644 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN B 644 "   -0.813 2.00e-02 2.50e+03
        pdb="HD22 ASN B 644 "    0.818 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 644 "   -0.162 2.00e-02 2.50e+03   4.80e-01 3.45e+03
        pdb=" CG  ASN A 644 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 644 "    0.159 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 644 "   -0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN A 644 "    0.813 2.00e-02 2.50e+03
        pdb="HD22 ASN A 644 "   -0.818 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 455 "   -0.245 2.00e-02 2.50e+03   8.72e-02 3.04e+02
        pdb=" CG  TRP A 455 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 455 "    0.047 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 455 "    0.035 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 455 "    0.075 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 455 "    0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 455 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 455 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 455 "    0.021 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 455 "   -0.051 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 455 "    0.103 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 455 "    0.120 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 455 "   -0.091 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 455 "    0.060 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 455 "   -0.081 2.00e-02 2.50e+03
  ... (remaining 1111 not shown)

  Histogram of nonbonded interaction distances:
        0.54 -     1.35: 1
        1.35 -     2.16: 475
        2.16 -     2.97: 19989
        2.97 -     3.79: 33969
        3.79 -     4.60: 54417
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 108851
  Sorted by model distance:
  nonbonded pdb=" H2  HOH A 803 "
            pdb=" H2  HOH B 803 "
     model   vdw
     0.536 2.100
  nonbonded pdb=" O   ARG A 567 "
            pdb=" H2  HOH A 801 "
     model   vdw
     1.440 2.450
  nonbonded pdb=" H2  HOH A 803 "
            pdb=" O   HOH B 803 "
     model   vdw
     1.474 2.450
  nonbonded pdb=" O   HOH A 803 "
            pdb=" H2  HOH B 803 "
     model   vdw
     1.475 2.450
  nonbonded pdb="HH22 ARG B 519 "
            pdb="HD21 ASN B 542 "
     model   vdw
     1.547 2.100
  ... (remaining 108846 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 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:             3.890
  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:             0.130
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.460
  Find NCS groups from input model:        0.100
  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:13.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
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      :  0.023   0.132   3898  Z= 1.240
  Angle     :  2.286  13.446   5326  Z= 1.471
  Chirality :  0.199   0.710    584
  Planarity :  0.014   0.078    684
  Dihedral  : 15.900  89.986   1400
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  6.76 %
    Favored  : 91.79 %
  Cbeta Deviations :  5.50 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.35), residues: 456
  helix: -2.80 (0.26), residues: 182
  sheet: -0.24 (0.62), residues: 56
  loop : -0.63 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.158   0.033   TRP A 455 
 HIS   0.009   0.005   HIS B 448 
 PHE   0.080   0.018   PHE B 580 
 TYR   0.111   0.026   TYR A 512 
 ARG   0.008   0.002   ARG A 535 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15991 (  175)
  hydrogen bonds       : angle       9.10724 (  471)
  covalent geometry    : bond        0.02298 ( 3898)
  covalent geometry    : angle       2.28570 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 0
  residues processed: 108
  average time/residue: 1.8791
  time to fit residues: 211.3451
Evaluate side-chains
  75 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 456 ASN
A 571 GLN
B 456 ASN
** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 610 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.193730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.179226 restraints weight = 11471.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 1.73
r_work: 0.4027 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3906 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3898  Z= 0.155
  Angle     :  0.608   5.415   5326  Z= 0.320
  Chirality :  0.041   0.157    584
  Planarity :  0.005   0.047    684
  Dihedral  :  5.527  16.535    492
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.77 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.36), residues: 456
  helix: -1.24 (0.34), residues: 188
  sheet: -0.02 (0.57), residues: 68
  loop : -1.21 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 591 
 HIS   0.003   0.002   HIS A 448 
 PHE   0.013   0.002   PHE B 564 
 TYR   0.008   0.002   TYR B 538 
 ARG   0.003   0.001   ARG B 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04315 (  175)
  hydrogen bonds       : angle       6.75597 (  471)
  covalent geometry    : bond        0.00351 ( 3898)
  covalent geometry    : angle       0.60806 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6864 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 94
  average time/residue: 2.2155
  time to fit residues: 215.5848
Evaluate side-chains
  79 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  601 GLU
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0270
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
A 485 GLN
A 571 GLN
B 485 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.193573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.179164 restraints weight = 11577.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 1.74
r_work: 0.4026 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3898  Z= 0.110
  Angle     :  0.537   5.478   5326  Z= 0.277
  Chirality :  0.040   0.151    584
  Planarity :  0.005   0.044    684
  Dihedral  :  4.825  13.784    492
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.84 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.38), residues: 456
  helix: -0.20 (0.38), residues: 176
  sheet:  0.10 (0.55), residues: 68
  loop : -0.48 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 591 
 HIS   0.004   0.002   HIS B 613 
 PHE   0.008   0.001   PHE A 617 
 TYR   0.006   0.001   TYR A 532 
 ARG   0.003   0.000   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  175)
  hydrogen bonds       : angle       5.99592 (  471)
  covalent geometry    : bond        0.00253 ( 3898)
  covalent geometry    : angle       0.53737 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: A  601 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7016 (mp0)
REVERT: B  567 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7577 (mtm110)
  outliers start: 7
  outliers final: 1
  residues processed: 83
  average time/residue: 2.2816
  time to fit residues: 195.9111
Evaluate side-chains
  78 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  601 GLU
Chi-restraints excluded: chain B residue  534 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 2 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN
B 571 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.192454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.177923 restraints weight = 11558.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4095 rms_B_bonded: 1.73
r_work: 0.4016 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3894 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3898  Z= 0.126
  Angle     :  0.542   5.614   5326  Z= 0.279
  Chirality :  0.040   0.149    584
  Planarity :  0.005   0.045    684
  Dihedral  :  4.624  14.365    492
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.08 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.38), residues: 456
  helix:  0.07 (0.39), residues: 176
  sheet:  0.03 (0.54), residues: 68
  loop : -0.39 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 561 
 HIS   0.004   0.001   HIS B 613 
 PHE   0.007   0.001   PHE B 617 
 TYR   0.008   0.001   TYR A 532 
 ARG   0.003   0.001   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03556 (  175)
  hydrogen bonds       : angle       5.69962 (  471)
  covalent geometry    : bond        0.00290 ( 3898)
  covalent geometry    : angle       0.54220 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7110 (ptp)
REVERT: A  567 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7565 (mtm-85)
REVERT: A  570 ILE cc_start: 0.8109 (mp) cc_final: 0.7873 (mm)
REVERT: B  442 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7129 (tt0)
REVERT: B  514 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6942 (tp30)
REVERT: B  567 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7564 (mtm110)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 1.9928
  time to fit residues: 180.3449
Evaluate side-chains
  79 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  514 GLU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  534 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0870
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 485 GLN
A 571 GLN
B 485 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.192371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.177786 restraints weight = 11462.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 1.70
r_work: 0.4024 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3906 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3898  Z= 0.117
  Angle     :  0.535   5.619   5326  Z= 0.274
  Chirality :  0.040   0.153    584
  Planarity :  0.005   0.041    684
  Dihedral  :  4.480  14.125    492
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.81 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.39), residues: 456
  helix:  0.29 (0.39), residues: 176
  sheet:  0.14 (0.54), residues: 68
  loop : -0.43 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 561 
 HIS   0.004   0.001   HIS B 613 
 PHE   0.007   0.001   PHE B 617 
 TYR   0.008   0.001   TYR A 532 
 ARG   0.002   0.000   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  175)
  hydrogen bonds       : angle       5.50957 (  471)
  covalent geometry    : bond        0.00275 ( 3898)
  covalent geometry    : angle       0.53505 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7478 (mtm110)
REVERT: A  570 ILE cc_start: 0.8147 (mp) cc_final: 0.7927 (mm)
REVERT: B  442 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7130 (tt0)
REVERT: B  514 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7040 (tp30)
REVERT: B  567 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7583 (mtm110)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 2.1165
  time to fit residues: 162.7156
Evaluate side-chains
  74 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  514 GLU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0470
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.192561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.178297 restraints weight = 11440.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 1.70
r_work: 0.4023 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3898  Z= 0.111
  Angle     :  0.523   5.630   5326  Z= 0.268
  Chirality :  0.040   0.152    584
  Planarity :  0.004   0.037    684
  Dihedral  :  4.339  14.262    492
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.05 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.39), residues: 456
  helix:  0.51 (0.40), residues: 176
  sheet:  0.10 (0.55), residues: 68
  loop : -0.38 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 561 
 HIS   0.004   0.001   HIS B 613 
 PHE   0.008   0.001   PHE A 617 
 TYR   0.007   0.001   TYR B 532 
 ARG   0.002   0.000   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  175)
  hydrogen bonds       : angle       5.34940 (  471)
  covalent geometry    : bond        0.00261 ( 3898)
  covalent geometry    : angle       0.52278 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7479 (mtm110)
REVERT: B  514 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7020 (tp30)
REVERT: B  567 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7562 (mtm110)
  outliers start: 5
  outliers final: 3
  residues processed: 75
  average time/residue: 2.1654
  time to fit residues: 168.4637
Evaluate side-chains
  78 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  514 GLU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.189855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.175175 restraints weight = 11492.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 1.69
r_work: 0.3997 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3880 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3898  Z= 0.145
  Angle     :  0.545   5.625   5326  Z= 0.279
  Chirality :  0.041   0.153    584
  Planarity :  0.005   0.035    684
  Dihedral  :  4.437  14.832    492
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 20.29 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.39), residues: 456
  helix:  0.40 (0.39), residues: 176
  sheet:  0.10 (0.55), residues: 68
  loop : -0.49 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 561 
 HIS   0.004   0.001   HIS B 613 
 PHE   0.008   0.002   PHE B 516 
 TYR   0.011   0.002   TYR A 532 
 ARG   0.002   0.000   ARG B 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  175)
  hydrogen bonds       : angle       5.47341 (  471)
  covalent geometry    : bond        0.00343 ( 3898)
  covalent geometry    : angle       0.54498 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7517 (mtm110)
REVERT: B  514 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7086 (tp30)
REVERT: B  567 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7578 (mtm110)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 2.2490
  time to fit residues: 186.5572
Evaluate side-chains
  75 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  514 GLU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.189061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.174501 restraints weight = 11545.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 1.73
r_work: 0.3978 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3898  Z= 0.148
  Angle     :  0.565   5.593   5326  Z= 0.292
  Chirality :  0.041   0.154    584
  Planarity :  0.005   0.040    684
  Dihedral  :  4.466  14.782    492
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.29 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.39), residues: 456
  helix:  0.43 (0.40), residues: 176
  sheet:  0.14 (0.55), residues: 68
  loop : -0.54 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 561 
 HIS   0.005   0.001   HIS B 613 
 PHE   0.008   0.001   PHE A 516 
 TYR   0.010   0.002   TYR A 532 
 ARG   0.003   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  175)
  hydrogen bonds       : angle       5.53351 (  471)
  covalent geometry    : bond        0.00352 ( 3898)
  covalent geometry    : angle       0.56543 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7514 (mtm110)
REVERT: B  514 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7027 (tp30)
REVERT: B  567 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7564 (mtm110)
  outliers start: 9
  outliers final: 3
  residues processed: 76
  average time/residue: 2.0641
  time to fit residues: 162.8901
Evaluate side-chains
  77 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  514 GLU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0050
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.191857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.177500 restraints weight = 11634.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 1.70
r_work: 0.4012 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.4236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3898  Z= 0.111
  Angle     :  0.528   5.628   5326  Z= 0.271
  Chirality :  0.040   0.152    584
  Planarity :  0.005   0.055    684
  Dihedral  :  4.298  14.955    492
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.53 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.40), residues: 456
  helix:  0.65 (0.40), residues: 176
  sheet:  0.22 (0.56), residues: 68
  loop : -0.39 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 561 
 HIS   0.004   0.001   HIS B 613 
 PHE   0.006   0.001   PHE A 617 
 TYR   0.006   0.001   TYR A 438 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03226 (  175)
  hydrogen bonds       : angle       5.27206 (  471)
  covalent geometry    : bond        0.00262 ( 3898)
  covalent geometry    : angle       0.52850 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7542 (mtm110)
REVERT: B  567 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7579 (mtm110)
  outliers start: 8
  outliers final: 4
  residues processed: 78
  average time/residue: 1.9350
  time to fit residues: 157.0623
Evaluate side-chains
  77 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.190126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.175715 restraints weight = 11594.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.4109 rms_B_bonded: 1.72
r_work: 0.4021 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3899 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3898  Z= 0.133
  Angle     :  0.552   5.630   5326  Z= 0.284
  Chirality :  0.041   0.155    584
  Planarity :  0.005   0.037    684
  Dihedral  :  4.349  15.011    492
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 21.50 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.40), residues: 456
  helix:  0.62 (0.40), residues: 176
  sheet:  0.25 (0.56), residues: 68
  loop : -0.44 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 561 
 HIS   0.005   0.001   HIS B 613 
 PHE   0.007   0.001   PHE A 516 
 TYR   0.009   0.001   TYR A 532 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03450 (  175)
  hydrogen bonds       : angle       5.35499 (  471)
  covalent geometry    : bond        0.00317 ( 3898)
  covalent geometry    : angle       0.55230 ( 5326)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7528 (mtm110)
REVERT: B  567 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7568 (mtm110)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 1.9701
  time to fit residues: 157.8274
Evaluate side-chains
  79 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.186878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.172268 restraints weight = 11591.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 1.68
r_work: 0.3997 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3874 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3898  Z= 0.174
  Angle     :  0.581   5.627   5326  Z= 0.300
  Chirality :  0.042   0.156    584
  Planarity :  0.005   0.056    684
  Dihedral  :  4.553  15.226    492
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 21.01 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.38), residues: 456
  helix:  0.45 (0.40), residues: 174
  sheet:  0.15 (0.55), residues: 68
  loop : -0.65 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 561 
 HIS   0.005   0.002   HIS A 613 
 PHE   0.009   0.002   PHE A 626 
 TYR   0.012   0.002   TYR B 532 
 ARG   0.003   0.000   ARG B 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  175)
  hydrogen bonds       : angle       5.63987 (  471)
  covalent geometry    : bond        0.00412 ( 3898)
  covalent geometry    : angle       0.58065 ( 5326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6675.62 seconds
wall clock time: 114 minutes 44.32 seconds (6884.32 seconds total)