Starting phenix.real_space_refine
on Mon Apr 28 10:27:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k3i_36852/04_2025/8k3i_36852.cif"
  }
  resolution = 2.83
  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=   0.005
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
     P       2      5.49       5
     S      24      5.16       5
     C    4682      2.51       5
     N    1300      2.21       5
     O    1364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7372
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3686
          Classifications: {'peptide': 480}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456}
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 75
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 82
    Chain: "B"
      Number of atoms: 3686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3686
          Classifications: {'peptide': 480}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456}
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 75
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 82
  Time building chain proxies: 8.37, per 1000 atoms: 1.14
  Number of scatterers: 7372
  At special positions: 0
  Unit cell: (102.09, 77.19, 78.02, 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      24     16.00
     P       2     15.00
     O    1364      8.00
     N    1300      7.00
     C    4682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1788

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      55.2% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 347
      removed outlier: 4.226A  pdb=" N   VAL A 343 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 368
    Processing helix  chain 'A' and resid 374 through 384
      removed outlier: 3.775A  pdb=" N   ALA A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 397
    Processing helix  chain 'A' and resid 398 through 415
      removed outlier: 4.002A  pdb=" N   VAL A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 413 " --> pdb=" O   PHE A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 455
    Processing helix  chain 'A' and resid 466 through 479
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 496 through 509
    Processing helix  chain 'A' and resid 525 through 536
      removed outlier: 4.068A  pdb=" N   ARG A 535 " --> pdb=" O   SER A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559
      removed outlier: 3.628A  pdb=" N   ARG A 557 " --> pdb=" O   GLN A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 590
    Processing helix  chain 'A' and resid 613 through 618
    Processing helix  chain 'A' and resid 644 through 659
      removed outlier: 4.359A  pdb=" N   GLU A 653 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 654 " --> pdb=" O   ARG A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 665
      No H-bonds generated for 'chain 'A' and resid 663 through 665'
    Processing helix  chain 'A' and resid 666 through 682
    Processing helix  chain 'A' and resid 688 through 693
      removed outlier: 3.634A  pdb=" N   LEU A 692 " --> pdb=" O   ASP A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 695
      No H-bonds generated for 'chain 'A' and resid 694 through 695'
    Processing helix  chain 'A' and resid 696 through 700
    Processing helix  chain 'A' and resid 702 through 738
    Processing helix  chain 'A' and resid 760 through 773
    Processing helix  chain 'A' and resid 780 through 783
    Processing helix  chain 'A' and resid 797 through 811
    Processing helix  chain 'B' and resid 337 through 347
      removed outlier: 4.223A  pdb=" N   VAL B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 368
    Processing helix  chain 'B' and resid 374 through 384
      removed outlier: 3.777A  pdb=" N   ALA B 378 " --> pdb=" O   ARG B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 397
    Processing helix  chain 'B' and resid 398 through 415
      removed outlier: 4.002A  pdb=" N   VAL B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE B 413 " --> pdb=" O   PHE B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 455
    Processing helix  chain 'B' and resid 466 through 479
    Processing helix  chain 'B' and resid 487 through 489
      No H-bonds generated for 'chain 'B' and resid 487 through 489'
    Processing helix  chain 'B' and resid 496 through 509
    Processing helix  chain 'B' and resid 525 through 536
      removed outlier: 4.068A  pdb=" N   ARG B 535 " --> pdb=" O   SER B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 559
      removed outlier: 3.627A  pdb=" N   ARG B 557 " --> pdb=" O   GLN B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 590
    Processing helix  chain 'B' and resid 613 through 618
    Processing helix  chain 'B' and resid 644 through 659
      removed outlier: 4.357A  pdb=" N   GLU B 653 " --> pdb=" O   SER B 649 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE B 654 " --> pdb=" O   ARG B 650 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 665
      No H-bonds generated for 'chain 'B' and resid 663 through 665'
    Processing helix  chain 'B' and resid 666 through 682
    Processing helix  chain 'B' and resid 688 through 693
      removed outlier: 3.638A  pdb=" N   LEU B 692 " --> pdb=" O   ASP B 688 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 693 " --> pdb=" O   GLN B 689 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 688 through 693'
    Processing helix  chain 'B' and resid 694 through 695
      No H-bonds generated for 'chain 'B' and resid 694 through 695'
    Processing helix  chain 'B' and resid 696 through 700
    Processing helix  chain 'B' and resid 702 through 738
    Processing helix  chain 'B' and resid 760 through 773
    Processing helix  chain 'B' and resid 780 through 783
    Processing helix  chain 'B' and resid 797 through 811
    Processing sheet with id=AA1, first strand: chain 'A' and resid 427 through 428
      removed outlier: 6.582A  pdb=" N   ILE A 427 " --> pdb=" O   SER A 775 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 494
      removed outlier: 6.071A  pdb=" N   ILE A 597 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL A 624 " --> pdb=" O   ILE A 597 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 624 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A 566 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   ASP A 600 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU A 568 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE A 519 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   GLN A 569 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   ALA A 521 " --> pdb=" O   GLN A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 546
    Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 742
    Processing sheet with id=AA5, first strand: chain 'B' and resid 427 through 428
      removed outlier: 6.583A  pdb=" N   ILE B 427 " --> pdb=" O   SER B 775 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 491 through 494
      removed outlier: 6.071A  pdb=" N   ILE B 597 " --> pdb=" O   ILE B 622 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   VAL B 624 " --> pdb=" O   ILE B 597 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU B 599 " --> pdb=" O   VAL B 624 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   SER B 626 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL B 566 " --> pdb=" O   ILE B 598 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   ASP B 600 " --> pdb=" O   VAL B 566 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU B 568 " --> pdb=" O   ASP B 600 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE B 519 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   GLN B 569 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   ALA B 521 " --> pdb=" O   GLN B 569 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 546
    Processing sheet with id=AA8, first strand: chain 'B' and resid 741 through 742

    385 hydrogen bonds defined for protein.
    1089 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: 3.08

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2327
        1.34 -     1.45: 1161
        1.45 -     1.57: 4014
        1.57 -     1.69: 2
        1.69 -     1.81: 38
  Bond restraints: 7542
  Sorted by residual:
  bond pdb=" OP4 LLP A 629 "
       pdb=" P   LLP A 629 "
    ideal  model  delta    sigma   weight residual
    1.726  1.540  0.186 2.00e-02 2.50e+03 8.64e+01
  bond pdb=" OP4 LLP B 629 "
       pdb=" P   LLP B 629 "
    ideal  model  delta    sigma   weight residual
    1.726  1.540  0.186 2.00e-02 2.50e+03 8.61e+01
  bond pdb=" NZ  LLP B 629 "
       pdb=" C4' LLP B 629 "
    ideal  model  delta    sigma   weight residual
    1.273  1.430 -0.157 2.00e-02 2.50e+03 6.19e+01
  bond pdb=" NZ  LLP A 629 "
       pdb=" C4' LLP A 629 "
    ideal  model  delta    sigma   weight residual
    1.273  1.429 -0.156 2.00e-02 2.50e+03 6.08e+01
  bond pdb=" C4  LLP A 629 "
       pdb=" C4' LLP A 629 "
    ideal  model  delta    sigma   weight residual
    1.464  1.614 -0.150 2.00e-02 2.50e+03 5.63e+01
  ... (remaining 7537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 10129
        2.19 -     4.37: 113
        4.37 -     6.56: 24
        6.56 -     8.75: 7
        8.75 -    10.93: 5
  Bond angle restraints: 10278
  Sorted by residual:
  angle pdb=" NZ  LLP B 629 "
        pdb=" C4' LLP B 629 "
        pdb=" C4  LLP B 629 "
      ideal   model   delta    sigma   weight residual
     120.09  109.16   10.93 3.00e+00 1.11e-01 1.33e+01
  angle pdb=" NZ  LLP A 629 "
        pdb=" C4' LLP A 629 "
        pdb=" C4  LLP A 629 "
      ideal   model   delta    sigma   weight residual
     120.09  109.17   10.92 3.00e+00 1.11e-01 1.32e+01
  angle pdb=" CE  LLP B 629 "
        pdb=" NZ  LLP B 629 "
        pdb=" C4' LLP B 629 "
      ideal   model   delta    sigma   weight residual
     119.26  109.80    9.46 3.00e+00 1.11e-01 9.94e+00
  angle pdb=" CE  LLP A 629 "
        pdb=" NZ  LLP A 629 "
        pdb=" C4' LLP A 629 "
      ideal   model   delta    sigma   weight residual
     119.26  109.85    9.41 3.00e+00 1.11e-01 9.84e+00
  angle pdb=" OP1 LLP A 629 "
        pdb=" P   LLP A 629 "
        pdb=" OP4 LLP A 629 "
      ideal   model   delta    sigma   weight residual
     100.47  109.23   -8.76 3.00e+00 1.11e-01 8.53e+00
  ... (remaining 10273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 4050
       17.32 -    34.64: 346
       34.64 -    51.95: 48
       51.95 -    69.27: 22
       69.27 -    86.59: 4
  Dihedral angle restraints: 4470
    sinusoidal: 1688
      harmonic: 2782
  Sorted by residual:
  dihedral pdb=" CA  GLU B 367 "
           pdb=" C   GLU B 367 "
           pdb=" N   LEU B 368 "
           pdb=" CA  LEU B 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.62   20.38     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  GLU A 367 "
           pdb=" C   GLU A 367 "
           pdb=" N   LEU A 368 "
           pdb=" CA  LEU A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.64   20.36     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  SER B 748 "
           pdb=" C   SER B 748 "
           pdb=" N   ILE B 749 "
           pdb=" CA  ILE B 749 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.46  -15.54     0      5.00e+00 4.00e-02 9.67e+00
  ... (remaining 4467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 695
       0.034 -    0.068: 332
       0.068 -    0.101: 100
       0.101 -    0.135: 35
       0.135 -    0.169: 2
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" CA  GLU A 367 "
            pdb=" N   GLU A 367 "
            pdb=" C   GLU A 367 "
            pdb=" CB  GLU A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.12e-01
  chirality pdb=" CA  GLU B 367 "
            pdb=" N   GLU B 367 "
            pdb=" C   GLU B 367 "
            pdb=" CB  GLU B 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CA  ILE A 687 "
            pdb=" N   ILE A 687 "
            pdb=" C   ILE A 687 "
            pdb=" CB  ILE A 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1161 not shown)

  Planarity restraints: 1324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 629 "    0.191 2.00e-02 2.50e+03   3.31e-01 1.10e+03
        pdb=" NZ  LLP B 629 "   -0.485 2.00e-02 2.50e+03
        pdb=" C4  LLP B 629 "   -0.102 2.00e-02 2.50e+03
        pdb=" C4' LLP B 629 "    0.396 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 629 "   -0.192 2.00e-02 2.50e+03   3.31e-01 1.10e+03
        pdb=" NZ  LLP A 629 "    0.486 2.00e-02 2.50e+03
        pdb=" C4  LLP A 629 "    0.101 2.00e-02 2.50e+03
        pdb=" C4' LLP A 629 "   -0.395 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 670 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.16e+00
        pdb=" C   VAL A 670 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   VAL A 670 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 671 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1321 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 48
        2.63 -     3.20: 6519
        3.20 -     3.76: 11642
        3.76 -     4.33: 16620
        4.33 -     4.90: 27399
  Nonbonded interactions: 62228
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 416 "
            pdb=" OH  TYR B 762 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" OD2 ASP A 416 "
            pdb=" OH  TYR A 762 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" O   ILE B 588 "
            pdb=" OG1 THR B 591 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   ILE A 588 "
            pdb=" OG1 THR A 591 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" NE2 HIS A 485 "
            pdb=" OE2 GLU A 487 "
     model   vdw
     2.353 3.120
  ... (remaining 62223 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: 0.03
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:             133.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     29.510
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:20.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  183.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
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      :  0.007   0.186   7542  Z= 0.321
  Angle     :  0.666  10.934  10278  Z= 0.323
  Chirality :  0.044   0.169   1164
  Planarity :  0.014   0.331   1324
  Dihedral  : 13.366  86.588   2682
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  0.64 (0.27), residues: 950
  helix:  1.52 (0.25), residues: 450
  sheet:  0.26 (0.45), residues: 126
  loop : -0.85 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 631 
 HIS   0.003   0.001   HIS B 485 
 PHE   0.023   0.002   PHE B 641 
 TYR   0.023   0.002   TYR B 458 
 ARG   0.004   0.000   ARG A 616 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14452 (  385)
  hydrogen bonds       : angle       6.10940 ( 1089)
  covalent geometry    : bond        0.00675 ( 7542)
  covalent geometry    : angle       0.66644 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.952 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 2.2433
  time to fit residues: 217.4938
Evaluate side-chains
  58 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
A 553 GLN
B 349 ASN
B 553 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.115555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.095994 restraints weight = 8336.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.20
r_work: 0.2861 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7542  Z= 0.160
  Angle     :  0.566   7.476  10278  Z= 0.292
  Chirality :  0.043   0.131   1164
  Planarity :  0.005   0.046   1324
  Dihedral  :  6.169  77.959   1084
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  7.12 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.15 (0.27), residues: 950
  helix:  2.02 (0.24), residues: 462
  sheet:  0.40 (0.45), residues: 124
  loop : -0.76 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 631 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.022   0.002   PHE B 641 
 TYR   0.012   0.002   TYR B 514 
 ARG   0.006   0.000   ARG A 693 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04952 (  385)
  hydrogen bonds       : angle       4.52757 ( 1089)
  covalent geometry    : bond        0.00375 ( 7542)
  covalent geometry    : angle       0.56589 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  447 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6245 (tt0)
REVERT: A  721 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7840 (tm-30)
REVERT: A  722 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7414 (mp10)
REVERT: A  806 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6903 (mm-30)
REVERT: B  447 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6265 (tt0)
  outliers start: 12
  outliers final: 0
  residues processed: 74
  average time/residue: 1.6285
  time to fit residues: 126.1097
Evaluate side-chains
  62 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain B residue  447 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 553 GLN
B 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.114800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.094692 restraints weight = 8489.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.28
r_work: 0.2828 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7542  Z= 0.168
  Angle     :  0.556   7.513  10278  Z= 0.287
  Chirality :  0.043   0.133   1164
  Planarity :  0.005   0.049   1324
  Dihedral  :  6.148  78.171   1084
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.76 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.23 (0.27), residues: 950
  helix:  2.11 (0.24), residues: 462
  sheet:  0.40 (0.45), residues: 124
  loop : -0.74 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 631 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.022   0.002   PHE B 641 
 TYR   0.012   0.002   TYR B 514 
 ARG   0.003   0.000   ARG A 616 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  385)
  hydrogen bonds       : angle       4.40744 ( 1089)
  covalent geometry    : bond        0.00397 ( 7542)
  covalent geometry    : angle       0.55569 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6974 (ptm160)
REVERT: A  447 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6217 (tt0)
REVERT: B  447 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6216 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 75
  average time/residue: 1.7302
  time to fit residues: 135.5023
Evaluate side-chains
  67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  447 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 553 GLN
B 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.114436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.094425 restraints weight = 8453.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.27
r_work: 0.2839 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7542  Z= 0.185
  Angle     :  0.571   7.475  10278  Z= 0.295
  Chirality :  0.044   0.134   1164
  Planarity :  0.005   0.054   1324
  Dihedral  :  6.196  78.156   1084
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.03 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.22 (0.27), residues: 950
  helix:  2.10 (0.24), residues: 462
  sheet:  0.40 (0.45), residues: 124
  loop : -0.74 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 631 
 HIS   0.004   0.001   HIS A 485 
 PHE   0.023   0.002   PHE A 641 
 TYR   0.011   0.002   TYR B 514 
 ARG   0.003   0.000   ARG A 616 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05177 (  385)
  hydrogen bonds       : angle       4.38834 ( 1089)
  covalent geometry    : bond        0.00440 ( 7542)
  covalent geometry    : angle       0.57057 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7034 (ptm160)
REVERT: A  447 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6192 (tt0)
REVERT: A  487 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7047 (pm20)
REVERT: A  721 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7969 (tm-30)
REVERT: B  447 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6052 (tt0)
REVERT: B  487 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7052 (pm20)
  outliers start: 18
  outliers final: 2
  residues processed: 78
  average time/residue: 1.7758
  time to fit residues: 144.4105
Evaluate side-chains
  71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  447 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 553 GLN
B 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.094382 restraints weight = 8360.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.27
r_work: 0.2826 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7542  Z= 0.184
  Angle     :  0.572   7.154  10278  Z= 0.295
  Chirality :  0.044   0.135   1164
  Planarity :  0.005   0.054   1324
  Dihedral  :  6.203  78.197   1084
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.89 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.21 (0.27), residues: 950
  helix:  2.11 (0.24), residues: 462
  sheet:  0.42 (0.45), residues: 124
  loop : -0.78 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 631 
 HIS   0.005   0.001   HIS A 485 
 PHE   0.023   0.002   PHE B 641 
 TYR   0.011   0.002   TYR B 514 
 ARG   0.004   0.000   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05145 (  385)
  hydrogen bonds       : angle       4.37522 ( 1089)
  covalent geometry    : bond        0.00439 ( 7542)
  covalent geometry    : angle       0.57209 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6993 (ptm160)
REVERT: A  407 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8180 (mp0)
REVERT: A  721 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7958 (tm-30)
REVERT: B  407 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8183 (mp0)
REVERT: B  487 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7039 (pm20)
  outliers start: 13
  outliers final: 2
  residues processed: 74
  average time/residue: 1.7610
  time to fit residues: 135.8816
Evaluate side-chains
  72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  407 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  407 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 553 GLN
B 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.116154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.096207 restraints weight = 8381.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.26
r_work: 0.2872 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7542  Z= 0.137
  Angle     :  0.516   6.407  10278  Z= 0.267
  Chirality :  0.041   0.130   1164
  Planarity :  0.005   0.047   1324
  Dihedral  :  6.099  80.071   1084
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.42 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.40 (0.27), residues: 950
  helix:  2.29 (0.24), residues: 462
  sheet:  0.44 (0.45), residues: 124
  loop : -0.70 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 631 
 HIS   0.005   0.001   HIS B 485 
 PHE   0.020   0.002   PHE A 641 
 TYR   0.010   0.001   TYR B 514 
 ARG   0.003   0.000   ARG B 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  385)
  hydrogen bonds       : angle       4.21467 ( 1089)
  covalent geometry    : bond        0.00319 ( 7542)
  covalent geometry    : angle       0.51626 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6976 (ptm160)
REVERT: A  407 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8140 (mp0)
REVERT: A  516 ASP cc_start: 0.8198 (m-30) cc_final: 0.7959 (m-30)
REVERT: A  721 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7981 (tm-30)
REVERT: B  407 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8175 (mp0)
REVERT: B  516 ASP cc_start: 0.8219 (m-30) cc_final: 0.7983 (m-30)
  outliers start: 14
  outliers final: 2
  residues processed: 74
  average time/residue: 1.7120
  time to fit residues: 132.2651
Evaluate side-chains
  68 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  407 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  407 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 553 GLN
B 553 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.117808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.097944 restraints weight = 8301.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.25
r_work: 0.2876 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7542  Z= 0.107
  Angle     :  0.476   5.916  10278  Z= 0.247
  Chirality :  0.040   0.128   1164
  Planarity :  0.004   0.046   1324
  Dihedral  :  6.010  81.575   1084
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.35 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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 (0.28), residues: 950
  helix:  2.49 (0.24), residues: 462
  sheet:  0.49 (0.45), residues: 120
  loop : -0.51 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 631 
 HIS   0.002   0.001   HIS B 712 
 PHE   0.018   0.001   PHE B 641 
 TYR   0.009   0.001   TYR B 514 
 ARG   0.003   0.000   ARG B 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  385)
  hydrogen bonds       : angle       4.06348 ( 1089)
  covalent geometry    : bond        0.00241 ( 7542)
  covalent geometry    : angle       0.47580 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6948 (ptm160)
REVERT: A  447 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6354 (tt0)
REVERT: A  516 ASP cc_start: 0.8164 (m-30) cc_final: 0.7937 (m-30)
REVERT: B  447 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6382 (tt0)
REVERT: B  516 ASP cc_start: 0.8206 (m-30) cc_final: 0.7979 (m-30)
  outliers start: 9
  outliers final: 1
  residues processed: 69
  average time/residue: 1.8567
  time to fit residues: 133.5275
Evaluate side-chains
  64 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  447 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 553 GLN
A 802 HIS
B 485 HIS
B 553 GLN
B 802 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.116014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.095784 restraints weight = 8409.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.28
r_work: 0.2876 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7542  Z= 0.156
  Angle     :  0.537   6.883  10278  Z= 0.278
  Chirality :  0.042   0.134   1164
  Planarity :  0.005   0.047   1324
  Dihedral  :  6.093  79.154   1084
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.69 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.46 (0.27), residues: 950
  helix:  2.38 (0.24), residues: 462
  sheet:  0.41 (0.45), residues: 124
  loop : -0.70 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 631 
 HIS   0.005   0.001   HIS A 485 
 PHE   0.021   0.002   PHE A 641 
 TYR   0.010   0.001   TYR B 652 
 ARG   0.002   0.000   ARG A 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  385)
  hydrogen bonds       : angle       4.20450 ( 1089)
  covalent geometry    : bond        0.00366 ( 7542)
  covalent geometry    : angle       0.53731 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7034 (ptm160)
REVERT: A  447 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6254 (tt0)
REVERT: A  516 ASP cc_start: 0.8243 (m-30) cc_final: 0.8020 (m-30)
REVERT: A  721 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8011 (tm-30)
REVERT: A  808 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8256 (mp)
REVERT: B  447 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6274 (tt0)
REVERT: B  516 ASP cc_start: 0.8268 (m-30) cc_final: 0.8038 (m-30)
  outliers start: 14
  outliers final: 4
  residues processed: 72
  average time/residue: 1.7316
  time to fit residues: 130.2632
Evaluate side-chains
  70 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  447 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 89 optimal weight:    0.3980
   chunk 9 optimal weight:    9.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 553 GLN
A 802 HIS
B 485 HIS
B 553 GLN
B 802 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.116980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.096924 restraints weight = 8406.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.26
r_work: 0.2931 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7542  Z= 0.126
  Angle     :  0.502   6.317  10278  Z= 0.261
  Chirality :  0.041   0.129   1164
  Planarity :  0.005   0.047   1324
  Dihedral  :  6.073  80.616   1084
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.08 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.60 (0.28), residues: 950
  helix:  2.47 (0.24), residues: 462
  sheet:  0.44 (0.45), residues: 120
  loop : -0.57 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 631 
 HIS   0.005   0.001   HIS B 485 
 PHE   0.019   0.002   PHE B 641 
 TYR   0.009   0.001   TYR B 514 
 ARG   0.002   0.000   ARG B 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04207 (  385)
  hydrogen bonds       : angle       4.10671 ( 1089)
  covalent geometry    : bond        0.00288 ( 7542)
  covalent geometry    : angle       0.50244 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  387 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7003 (ptm160)
REVERT: A  447 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6351 (tt0)
REVERT: A  516 ASP cc_start: 0.8207 (m-30) cc_final: 0.7984 (m-30)
REVERT: A  808 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: B  447 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6360 (tt0)
REVERT: B  516 ASP cc_start: 0.8254 (m-30) cc_final: 0.8034 (m-30)
REVERT: B  808 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8237 (mp)
  outliers start: 14
  outliers final: 2
  residues processed: 70
  average time/residue: 1.6879
  time to fit residues: 123.4153
Evaluate side-chains
  67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  808 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 553 GLN
A 802 HIS
B 485 HIS
B 553 GLN
B 802 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.116162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.096046 restraints weight = 8384.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.28
r_work: 0.2852 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7542  Z= 0.144
  Angle     :  0.525   6.601  10278  Z= 0.272
  Chirality :  0.042   0.132   1164
  Planarity :  0.005   0.047   1324
  Dihedral  :  6.079  79.633   1084
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.48 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.55 (0.27), residues: 950
  helix:  2.42 (0.24), residues: 462
  sheet:  0.42 (0.45), residues: 120
  loop : -0.58 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 631 
 HIS   0.005   0.001   HIS B 485 
 PHE   0.020   0.002   PHE B 641 
 TYR   0.010   0.001   TYR B 652 
 ARG   0.002   0.000   ARG B 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04514 (  385)
  hydrogen bonds       : angle       4.16145 ( 1089)
  covalent geometry    : bond        0.00337 ( 7542)
  covalent geometry    : angle       0.52456 (10278)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6994 (ptm160)
REVERT: A  447 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6251 (tt0)
REVERT: A  516 ASP cc_start: 0.8235 (m-30) cc_final: 0.8009 (m-30)
REVERT: A  808 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: B  447 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6263 (tt0)
REVERT: B  516 ASP cc_start: 0.8268 (m-30) cc_final: 0.8035 (m-30)
REVERT: B  808 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (mp)
  outliers start: 12
  outliers final: 4
  residues processed: 69
  average time/residue: 1.7855
  time to fit residues: 128.6817
Evaluate side-chains
  69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  387 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  808 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 37 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 553 GLN
A 802 HIS
B 485 HIS
B 553 GLN
B 802 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.118207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.098877 restraints weight = 8293.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.20
r_work: 0.2892 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7542  Z= 0.107
  Angle     :  0.476   5.715  10278  Z= 0.248
  Chirality :  0.040   0.126   1164
  Planarity :  0.004   0.046   1324
  Dihedral  :  5.998  81.953   1084
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.48 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.76 (0.28), residues: 950
  helix:  2.56 (0.24), residues: 464
  sheet:  0.55 (0.45), residues: 120
  loop : -0.46 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 631 
 HIS   0.003   0.001   HIS B 485 
 PHE   0.018   0.001   PHE B 641 
 TYR   0.008   0.001   TYR B 514 
 ARG   0.002   0.000   ARG B 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  385)
  hydrogen bonds       : angle       3.99276 ( 1089)
  covalent geometry    : bond        0.00240 ( 7542)
  covalent geometry    : angle       0.47599 (10278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5757.07 seconds
wall clock time: 100 minutes 36.34 seconds (6036.34 seconds total)