Starting phenix.real_space_refine
on Fri Dec 27 21:06:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7d_28903/12_2024/8f7d_28903.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.044
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4234      2.51       5
     N    1130      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6578
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "F"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3257
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 17, 'TRANS': 386}
  Time building chain proxies: 5.83, per 1000 atoms: 0.89
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (110.04, 73.36, 82.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1190      8.00
     N    1130      7.00
     C    4234      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: 1.58
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      33.2% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 445
      removed outlier: 3.724A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 468
    Processing helix  chain 'A' and resid 484 through 495
    Processing helix  chain 'A' and resid 509 through 515
      removed outlier: 3.635A  pdb=" N   ILE A 512 " --> pdb=" O   PRO A 509 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR A 513 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A 515 " --> pdb=" O   ILE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 542
      removed outlier: 4.238A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.912A  pdb=" N   LYS A 588 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS A 589 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 585 through 589'
    Processing helix  chain 'A' and resid 633 through 638
      removed outlier: 3.508A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS A 637 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
      removed outlier: 3.628A  pdb=" N   ILE A 658 " --> pdb=" O   PRO A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 684
      removed outlier: 3.568A  pdb=" N   CYS A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 707
      removed outlier: 3.771A  pdb=" N   ILE A 704 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 730
      removed outlier: 3.936A  pdb=" N   PHE A 728 " --> pdb=" O   PRO A 724 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   CYS A 730 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 753
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 787 through 793
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'F' and resid 401 through 409
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 437 through 443
      removed outlier: 3.922A  pdb=" N   PHE F 441 " --> pdb=" O   PRO F 437 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE F 443 " --> pdb=" O   THR F 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 460 through 466
      removed outlier: 3.946A  pdb=" N   ILE F 463 " --> pdb=" O   PRO F 460 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 482 through 492
    Processing helix  chain 'F' and resid 509 through 513
      removed outlier: 3.834A  pdb=" N   LEU F 513 " --> pdb=" O   MET F 510 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 534 through 538
      removed outlier: 3.801A  pdb=" N   SER F 537 " --> pdb=" O   THR F 534 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 557 through 564
      removed outlier: 3.711A  pdb=" N   VAL F 561 " --> pdb=" O   PRO F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 582 through 587
    Processing helix  chain 'F' and resid 605 through 611
      removed outlier: 4.098A  pdb=" N   PHE F 609 " --> pdb=" O   PRO F 605 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 629 through 636
      removed outlier: 3.524A  pdb=" N   SER F 632 " --> pdb=" O   GLU F 629 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLN F 634 " --> pdb=" O   VAL F 631 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 653 through 659
      removed outlier: 3.934A  pdb=" N   ILE F 656 " --> pdb=" O   PRO F 653 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU F 659 " --> pdb=" O   ILE F 656 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 699 through 705
      removed outlier: 3.699A  pdb=" N   ILE F 702 " --> pdb=" O   PRO F 699 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 723 through 728
    Processing helix  chain 'F' and resid 745 through 749
      removed outlier: 3.540A  pdb=" N   ILE F 748 " --> pdb=" O   SER F 745 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLY F 749 " --> pdb=" O   PRO F 746 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 745 through 749'
    Processing helix  chain 'F' and resid 768 through 772
      removed outlier: 4.126A  pdb=" N   LEU F 771 " --> pdb=" O   PRO F 768 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY F 772 " --> pdb=" O   PRO F 769 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 768 through 772'
    Processing helix  chain 'F' and resid 785 through 790
    Processing helix  chain 'F' and resid 793 through 802
      removed outlier: 3.817A  pdb=" N   ALA F 802 " --> pdb=" O   GLU F 798 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.824A  pdb=" N   LEU A 474 " --> pdb=" O   HIS A 499 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LYS A 501 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU A 521 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   LYS A 552 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A 523 " --> pdb=" O   LYS A 552 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU A 572 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   ILE A 574 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 620
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668
      removed outlier: 7.012A  pdb=" N   LEU A 667 " --> pdb=" O   ASP A 691 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 737
      removed outlier: 6.818A  pdb=" N   LEU A 736 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE A 759 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 419 through 420
      removed outlier: 5.701A  pdb=" N   LEU F 426 " --> pdb=" O   SER F 448 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS F 450 " --> pdb=" O   LEU F 426 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   LEU F 428 " --> pdb=" O   LYS F 450 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU F 449 " --> pdb=" O   CYS F 473 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   HIS F 475 " --> pdb=" O   LEU F 449 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU F 451 " --> pdb=" O   HIS F 475 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU F 472 " --> pdb=" O   SER F 497 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   LEU F 474 " --> pdb=" O   LYS F 499 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   MET F 570 " --> pdb=" O   GLU F 595 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL F 597 " --> pdb=" O   MET F 570 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   VAL F 572 " --> pdb=" O   VAL F 597 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU F 594 " --> pdb=" O   ASP F 618 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LYS F 620 " --> pdb=" O   LEU F 594 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LEU F 596 " --> pdb=" O   LYS F 620 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   LEU F 617 " --> pdb=" O   LYS F 643 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LEU F 688 " --> pdb=" O   SER F 712 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   PHE F 711 " --> pdb=" O   LYS F 735 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 457 through 458
      removed outlier: 6.568A  pdb=" N   VAL F 457 " --> pdb=" O   LYS F 480 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    148 hydrogen bonds defined for protein.
    321 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: 2.49

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1913
        1.34 -     1.46: 916
        1.46 -     1.58: 3829
        1.58 -     1.70: 1
        1.70 -     1.82: 34
  Bond restraints: 6693
  Sorted by residual:
  bond pdb=" N   ASN A 423 "
       pdb=" CA  ASN A 423 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.17e-02 7.31e+03 9.47e+00
  bond pdb=" N   TRP F 645 "
       pdb=" CA  TRP F 645 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.16e-02 7.43e+03 9.06e+00
  bond pdb=" N   THR A 412 "
       pdb=" CA  THR A 412 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.21e-02 6.83e+03 7.87e+00
  bond pdb=" N   LYS A 422 "
       pdb=" CA  LYS A 422 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.25e-02 6.40e+03 7.75e+00
  bond pdb=" N   LEU A 430 "
       pdb=" CA  LEU A 430 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.21e-02 6.83e+03 7.36e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 8725
        2.35 -     4.69: 286
        4.69 -     7.04: 32
        7.04 -     9.38: 15
        9.38 -    11.73: 4
  Bond angle restraints: 9062
  Sorted by residual:
  angle pdb=" CB  MET F 432 "
        pdb=" CG  MET F 432 "
        pdb=" SD  MET F 432 "
      ideal   model   delta    sigma   weight residual
     112.70  124.43  -11.73 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" CB  GLU A 449 "
        pdb=" CG  GLU A 449 "
        pdb=" CD  GLU A 449 "
      ideal   model   delta    sigma   weight residual
     112.60  119.20   -6.60 1.70e+00 3.46e-01 1.51e+01
  angle pdb=" CA  MET A 434 "
        pdb=" CB  MET A 434 "
        pdb=" CG  MET A 434 "
      ideal   model   delta    sigma   weight residual
     114.10  121.60   -7.50 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CA  LYS A 622 "
        pdb=" CB  LYS A 622 "
        pdb=" CG  LYS A 622 "
      ideal   model   delta    sigma   weight residual
     114.10  121.58   -7.48 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  PHE A 433 "
        pdb=" C   PHE A 433 "
        pdb=" O   PHE A 433 "
      ideal   model   delta    sigma   weight residual
     120.71  116.75    3.96 1.06e+00 8.90e-01 1.40e+01
  ... (remaining 9057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3658
       17.87 -    35.75: 389
       35.75 -    53.62: 90
       53.62 -    71.50: 14
       71.50 -    89.37: 5
  Dihedral angle restraints: 4156
    sinusoidal: 1754
      harmonic: 2402
  Sorted by residual:
  dihedral pdb=" CA  LYS F 587 "
           pdb=" C   LYS F 587 "
           pdb=" N   MET F 588 "
           pdb=" CA  MET F 588 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  GLU F 505 "
           pdb=" C   GLU F 505 "
           pdb=" N   LEU F 506 "
           pdb=" CA  LEU F 506 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  SER F 677 "
           pdb=" C   SER F 677 "
           pdb=" N   HIS F 678 "
           pdb=" CA  HIS F 678 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.54  -19.46     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1011
       0.098 -    0.195: 71
       0.195 -    0.293: 1
       0.293 -    0.391: 0
       0.391 -    0.488: 1
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" CB  ILE A 629 "
            pdb=" CA  ILE A 629 "
            pdb=" CG1 ILE A 629 "
            pdb=" CG2 ILE A 629 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.16    0.49 2.00e-01 2.50e+01 5.96e+00
  chirality pdb=" CB  ILE F 759 "
            pdb=" CA  ILE F 759 "
            pdb=" CG1 ILE F 759 "
            pdb=" CG2 ILE F 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CG  LEU A 723 "
            pdb=" CB  LEU A 723 "
            pdb=" CD1 LEU A 723 "
            pdb=" CD2 LEU A 723 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.12e-01
  ... (remaining 1081 not shown)

  Planarity restraints: 1137
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 475 "   -0.032 2.00e-02 2.50e+03   2.92e-02 2.13e+01
        pdb=" CG  TRP A 475 "    0.080 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 475 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 475 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 475 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 475 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 475 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 475 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 475 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 475 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 687 "    0.023 2.00e-02 2.50e+03   2.11e-02 8.94e+00
        pdb=" CG  TYR F 687 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 687 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 687 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 687 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 687 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 687 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 687 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 488 "    0.012 2.00e-02 2.50e+03   1.81e-02 5.71e+00
        pdb=" CG  PHE F 488 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 488 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 488 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 488 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 488 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 488 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1134 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1456
        2.79 -     3.32: 6490
        3.32 -     3.85: 11415
        3.85 -     4.37: 14419
        4.37 -     4.90: 22616
  Nonbonded interactions: 56396
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 689 "
            pdb=" OG  SER F 691 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ILE F 556 "
            pdb=" ND2 ASN F 584 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   ARG F 775 "
            pdb=" NH1 ARG F 775 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   THR F 640 "
            pdb=" N   ARG F 664 "
     model   vdw
     2.334 3.120
  ... (remaining 56391 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.580
  Find NCS groups from input model:        0.100
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
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      :  0.005   0.102   6693  Z= 0.335
  Angle     :  0.997  11.731   9062  Z= 0.556
  Chirality :  0.053   0.488   1084
  Planarity :  0.005   0.041   1137
  Dihedral  : 15.553  89.372   2580
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 19.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 20.79 %
    Favored  : 78.68 %
  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: -2.71 (0.28), residues: 807
  helix: -2.79 (0.28), residues: 248
  sheet: -2.12 (0.53), residues: 113
  loop : -0.99 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.005   TRP A 475 
 HIS   0.007   0.001   HIS F 669 
 PHE   0.041   0.002   PHE F 488 
 TYR   0.053   0.003   TYR F 687 
 ARG   0.004   0.001   ARG A 671 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 280
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.8016 (tp) cc_final: 0.7760 (tp)
REVERT: A  551 LEU cc_start: 0.8946 (mt) cc_final: 0.8682 (mm)
REVERT: A  572 LEU cc_start: 0.8671 (tp) cc_final: 0.8408 (tp)
REVERT: A  592 ASN cc_start: 0.8153 (m-40) cc_final: 0.7555 (t0)
REVERT: A  645 LYS cc_start: 0.8899 (mttt) cc_final: 0.8550 (mttp)
REVERT: A  703 ASP cc_start: 0.7274 (m-30) cc_final: 0.6877 (t0)
REVERT: F  423 HIS cc_start: 0.7386 (m90) cc_final: 0.7132 (m-70)
REVERT: F  430 LEU cc_start: 0.8000 (mt) cc_final: 0.7799 (mp)
REVERT: F  446 LEU cc_start: 0.8320 (mt) cc_final: 0.8035 (mt)
REVERT: F  476 GLN cc_start: 0.8630 (mp10) cc_final: 0.8280 (mp10)
REVERT: F  496 LEU cc_start: 0.7806 (tp) cc_final: 0.7538 (tp)
REVERT: F  524 SER cc_start: 0.6946 (p) cc_final: 0.6098 (p)
REVERT: F  581 MET cc_start: 0.6333 (tpt) cc_final: 0.5908 (tpp)
REVERT: F  598 HIS cc_start: 0.7199 (t-170) cc_final: 0.6853 (t-170)
REVERT: F  666 PHE cc_start: 0.8759 (m-80) cc_final: 0.6929 (m-80)
REVERT: F  715 CYS cc_start: 0.6487 (m) cc_final: 0.6146 (m)
REVERT: F  726 TYR cc_start: 0.6646 (m-80) cc_final: 0.6253 (m-80)
REVERT: F  784 VAL cc_start: 0.6124 (m) cc_final: 0.5588 (m)
REVERT: F  800 MET cc_start: 0.3332 (tpt) cc_final: 0.2796 (mmt)
  outliers start: 4
  outliers final: 0
  residues processed: 282
  average time/residue: 0.2577
  time to fit residues: 90.7830
Evaluate side-chains
  159 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0270
   chunk 38 optimal weight:    0.3980
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.5440

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

Flipped N/Q/H residues before XYZ refinement:
A 409 ASN
A 636 GLN
A 650 HIS
F 407 ASN
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
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      :  0.004   0.047   6693  Z= 0.247
  Angle     :  0.801   9.984   9062  Z= 0.394
  Chirality :  0.047   0.190   1084
  Planarity :  0.005   0.044   1137
  Dihedral  :  5.277  21.062    864
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  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: -2.70 (0.29), residues: 807
  helix: -2.73 (0.27), residues: 261
  sheet: -2.73 (0.46), residues: 141
  loop : -0.54 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.006   TRP A 803 
 HIS   0.010   0.001   HIS A 431 
 PHE   0.035   0.003   PHE F 609 
 TYR   0.023   0.003   TYR F 710 
 ARG   0.005   0.001   ARG A 765 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6519 (mm-30)
REVERT: A  495 LEU cc_start: 0.8545 (tp) cc_final: 0.8300 (tp)
REVERT: A  498 LEU cc_start: 0.8952 (tp) cc_final: 0.8737 (mt)
REVERT: A  500 ILE cc_start: 0.8753 (mm) cc_final: 0.8502 (mp)
REVERT: A  572 LEU cc_start: 0.8700 (tp) cc_final: 0.8245 (tp)
REVERT: A  576 ASN cc_start: 0.9415 (m110) cc_final: 0.9118 (t0)
REVERT: A  592 ASN cc_start: 0.8456 (m-40) cc_final: 0.8055 (t0)
REVERT: A  687 LEU cc_start: 0.8390 (mt) cc_final: 0.8087 (mt)
REVERT: A  689 TYR cc_start: 0.8012 (m-80) cc_final: 0.7768 (m-80)
REVERT: A  713 LEU cc_start: 0.8738 (tp) cc_final: 0.8065 (pp)
REVERT: A  728 PHE cc_start: 0.8426 (m-80) cc_final: 0.7505 (m-80)
REVERT: A  769 LEU cc_start: 0.8610 (mt) cc_final: 0.8207 (tp)
REVERT: A  780 LYS cc_start: 0.7286 (pttt) cc_final: 0.7081 (pttm)
REVERT: F  423 HIS cc_start: 0.7841 (m90) cc_final: 0.7442 (m-70)
REVERT: F  446 LEU cc_start: 0.8270 (mt) cc_final: 0.7827 (mt)
REVERT: F  573 HIS cc_start: 0.7889 (m90) cc_final: 0.7466 (m-70)
REVERT: F  579 LEU cc_start: 0.5517 (tp) cc_final: 0.5305 (tp)
REVERT: F  598 HIS cc_start: 0.7642 (t-170) cc_final: 0.7350 (t-170)
REVERT: F  617 LEU cc_start: 0.7005 (tp) cc_final: 0.6563 (pp)
REVERT: F  618 ASP cc_start: 0.6876 (t0) cc_final: 0.6566 (t70)
REVERT: F  643 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8763 (tptp)
REVERT: F  666 PHE cc_start: 0.9082 (m-80) cc_final: 0.7378 (m-10)
REVERT: F  732 LYS cc_start: 0.8728 (mmtp) cc_final: 0.7909 (mmtt)
REVERT: F  778 LYS cc_start: 0.4917 (mmmt) cc_final: 0.4619 (mmtm)
REVERT: F  786 ASP cc_start: 0.2932 (p0) cc_final: 0.1597 (t0)
REVERT: F  800 MET cc_start: 0.3318 (tpt) cc_final: 0.2881 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2077
  time to fit residues: 56.0600
Evaluate side-chains
  139 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0570
   chunk 60 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.3702

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

Flipped N/Q/H residues before XYZ refinement:
** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 ASN
F 402 GLN
** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 635 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6693  Z= 0.275
  Angle     :  0.750   9.800   9062  Z= 0.374
  Chirality :  0.046   0.186   1084
  Planarity :  0.005   0.051   1137
  Dihedral  :  5.141  23.855    864
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 22.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.47 %
    Favored  : 95.39 %
  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: -2.62 (0.30), residues: 807
  helix: -2.60 (0.28), residues: 263
  sheet: -2.67 (0.47), residues: 136
  loop : -0.58 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.005   TRP A 803 
 HIS   0.011   0.001   HIS F 678 
 PHE   0.024   0.002   PHE F 609 
 TYR   0.024   0.002   TYR F 520 
 ARG   0.008   0.001   ARG A 492 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8408 (pt0) cc_final: 0.7889 (pm20)
REVERT: A  435 LEU cc_start: 0.8156 (mt) cc_final: 0.7300 (mt)
REVERT: A  436 SER cc_start: 0.9229 (m) cc_final: 0.8966 (t)
REVERT: A  465 ILE cc_start: 0.8442 (tt) cc_final: 0.7977 (tt)
REVERT: A  495 LEU cc_start: 0.8555 (tp) cc_final: 0.8200 (tp)
REVERT: A  498 LEU cc_start: 0.9110 (tp) cc_final: 0.8783 (mt)
REVERT: A  500 ILE cc_start: 0.8906 (mm) cc_final: 0.8629 (mp)
REVERT: A  518 LEU cc_start: 0.8205 (tp) cc_final: 0.7774 (tp)
REVERT: A  576 ASN cc_start: 0.9408 (m-40) cc_final: 0.9086 (t0)
REVERT: A  592 ASN cc_start: 0.8405 (m-40) cc_final: 0.7806 (t0)
REVERT: A  665 GLU cc_start: 0.8837 (tt0) cc_final: 0.8455 (tm-30)
REVERT: A  687 LEU cc_start: 0.8559 (mt) cc_final: 0.8230 (mt)
REVERT: A  713 LEU cc_start: 0.8892 (tp) cc_final: 0.7988 (pp)
REVERT: A  728 PHE cc_start: 0.7774 (m-80) cc_final: 0.7488 (m-80)
REVERT: A  762 ARG cc_start: 0.5761 (ttt90) cc_final: 0.5506 (ttt-90)
REVERT: A  780 LYS cc_start: 0.7533 (pttt) cc_final: 0.7274 (pttm)
REVERT: F  403 LEU cc_start: 0.8316 (tt) cc_final: 0.7814 (mm)
REVERT: F  426 LEU cc_start: 0.7648 (tp) cc_final: 0.7068 (tp)
REVERT: F  581 MET cc_start: 0.8096 (tpp) cc_final: 0.7810 (tpp)
REVERT: F  598 HIS cc_start: 0.7572 (t-170) cc_final: 0.7314 (t-170)
REVERT: F  617 LEU cc_start: 0.6869 (tp) cc_final: 0.6530 (pp)
REVERT: F  618 ASP cc_start: 0.7544 (t0) cc_final: 0.6014 (t70)
REVERT: F  778 LYS cc_start: 0.4976 (mmmt) cc_final: 0.4713 (mmtm)
REVERT: F  800 MET cc_start: 0.3231 (tpt) cc_final: 0.2729 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2161
  time to fit residues: 49.8634
Evaluate side-chains
  125 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0870
   chunk 64 optimal weight:    9.9990
   overall best weight:    1.3160

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 416 GLN
F 482 HIS
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.6439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6693  Z= 0.249
  Angle     :  0.727   9.119   9062  Z= 0.362
  Chirality :  0.046   0.150   1084
  Planarity :  0.005   0.053   1137
  Dihedral  :  5.044  25.142    864
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 21.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  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: -2.70 (0.29), residues: 807
  helix: -2.54 (0.29), residues: 252
  sheet: -2.78 (0.43), residues: 150
  loop : -0.65 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.006   TRP A 803 
 HIS   0.006   0.001   HIS A 694 
 PHE   0.030   0.002   PHE F 666 
 TYR   0.020   0.002   TYR F 726 
 ARG   0.004   0.001   ARG A 666 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 155
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8416 (pt0) cc_final: 0.8090 (pt0)
REVERT: A  436 SER cc_start: 0.9029 (m) cc_final: 0.8744 (t)
REVERT: A  473 GLU cc_start: 0.8126 (tt0) cc_final: 0.7895 (tt0)
REVERT: A  560 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5875 (tm-30)
REVERT: A  576 ASN cc_start: 0.9425 (m-40) cc_final: 0.9095 (m-40)
REVERT: A  592 ASN cc_start: 0.8280 (m-40) cc_final: 0.7659 (t0)
REVERT: A  595 GLU cc_start: 0.8746 (mp0) cc_final: 0.8450 (mp0)
REVERT: A  687 LEU cc_start: 0.8618 (mt) cc_final: 0.8270 (mt)
REVERT: A  713 LEU cc_start: 0.8870 (tp) cc_final: 0.8011 (pp)
REVERT: A  728 PHE cc_start: 0.7920 (m-80) cc_final: 0.7710 (m-80)
REVERT: A  780 LYS cc_start: 0.7666 (pttt) cc_final: 0.7391 (pttm)
REVERT: F  403 LEU cc_start: 0.8308 (tt) cc_final: 0.7754 (mm)
REVERT: F  430 LEU cc_start: 0.7875 (mp) cc_final: 0.7627 (mp)
REVERT: F  439 THR cc_start: 0.8444 (t) cc_final: 0.8237 (m)
REVERT: F  446 LEU cc_start: 0.8347 (mt) cc_final: 0.7993 (mt)
REVERT: F  581 MET cc_start: 0.8059 (tpp) cc_final: 0.7654 (tpp)
REVERT: F  598 HIS cc_start: 0.7493 (t-170) cc_final: 0.7188 (t-170)
REVERT: F  666 PHE cc_start: 0.9051 (m-80) cc_final: 0.7394 (m-10)
REVERT: F  759 ILE cc_start: 0.7574 (mm) cc_final: 0.7285 (mm)
REVERT: F  778 LYS cc_start: 0.5111 (mmmt) cc_final: 0.4558 (mmtm)
REVERT: F  800 MET cc_start: 0.2834 (tpt) cc_final: 0.2451 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1888
  time to fit residues: 39.4280
Evaluate side-chains
  121 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 69 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 HIS
** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 482 HIS
F 573 HIS
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.6994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6693  Z= 0.242
  Angle     :  0.742  11.843   9062  Z= 0.362
  Chirality :  0.046   0.238   1084
  Planarity :  0.005   0.049   1137
  Dihedral  :  5.016  24.456    864
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 22.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.82 %
    Favored  : 96.05 %
  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: -2.91 (0.29), residues: 807
  helix: -2.71 (0.27), residues: 260
  sheet: -2.85 (0.41), residues: 156
  loop : -0.72 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.006   TRP A 803 
 HIS   0.008   0.001   HIS F 475 
 PHE   0.022   0.002   PHE A 635 
 TYR   0.031   0.003   TYR F 687 
 ARG   0.004   0.001   ARG A 496 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8412 (pt0) cc_final: 0.8089 (pt0)
REVERT: A  436 SER cc_start: 0.8990 (m) cc_final: 0.8640 (t)
REVERT: A  571 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7207 (mptt)
REVERT: A  576 ASN cc_start: 0.9463 (m-40) cc_final: 0.9166 (m-40)
REVERT: A  592 ASN cc_start: 0.8209 (m-40) cc_final: 0.7595 (t0)
REVERT: A  595 GLU cc_start: 0.8780 (mp0) cc_final: 0.8297 (mp0)
REVERT: A  687 LEU cc_start: 0.8685 (mt) cc_final: 0.8328 (mt)
REVERT: A  713 LEU cc_start: 0.8743 (tp) cc_final: 0.7875 (pp)
REVERT: A  780 LYS cc_start: 0.7798 (pttt) cc_final: 0.7515 (pttm)
REVERT: F  573 HIS cc_start: 0.7756 (m-70) cc_final: 0.7534 (m-70)
REVERT: F  581 MET cc_start: 0.8135 (tpp) cc_final: 0.7754 (tpp)
REVERT: F  666 PHE cc_start: 0.8801 (m-80) cc_final: 0.8401 (m-10)
REVERT: F  759 ILE cc_start: 0.7433 (mm) cc_final: 0.7161 (mm)
REVERT: F  778 LYS cc_start: 0.5200 (mmmt) cc_final: 0.4603 (mmtm)
REVERT: F  800 MET cc_start: 0.2069 (tpt) cc_final: 0.1809 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1693
  time to fit residues: 35.9747
Evaluate side-chains
  122 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    0.0770
   chunk 15 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 478 HIS
A 560 GLN
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 423 HIS
F 475 HIS
F 482 HIS
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.7284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6693  Z= 0.186
  Angle     :  0.665   9.470   9062  Z= 0.331
  Chirality :  0.045   0.259   1084
  Planarity :  0.004   0.046   1137
  Dihedral  :  4.798  24.119    864
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.24 %
    Favored  : 97.50 %
  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: -2.83 (0.29), residues: 807
  helix: -2.63 (0.28), residues: 259
  sheet: -2.98 (0.40), residues: 156
  loop : -0.59 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.006   TRP A 803 
 HIS   0.005   0.001   HIS F 475 
 PHE   0.017   0.002   PHE F 667 
 TYR   0.015   0.002   TYR F 710 
 ARG   0.003   0.001   ARG A 749 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8338 (pt0) cc_final: 0.7979 (pt0)
REVERT: A  434 MET cc_start: 0.8766 (mmm) cc_final: 0.8556 (mmm)
REVERT: A  435 LEU cc_start: 0.8226 (mm) cc_final: 0.7987 (mm)
REVERT: A  436 SER cc_start: 0.8943 (m) cc_final: 0.8581 (t)
REVERT: A  520 GLU cc_start: 0.8317 (tt0) cc_final: 0.8092 (tt0)
REVERT: A  576 ASN cc_start: 0.9460 (m-40) cc_final: 0.9094 (m-40)
REVERT: A  592 ASN cc_start: 0.8054 (m-40) cc_final: 0.7471 (t0)
REVERT: A  683 TYR cc_start: 0.7402 (t80) cc_final: 0.7159 (t80)
REVERT: A  687 LEU cc_start: 0.8692 (mt) cc_final: 0.8305 (mt)
REVERT: A  713 LEU cc_start: 0.8786 (tp) cc_final: 0.7802 (pp)
REVERT: A  760 GLU cc_start: 0.8284 (pt0) cc_final: 0.8068 (pt0)
REVERT: A  779 LEU cc_start: 0.8138 (mt) cc_final: 0.7928 (mt)
REVERT: A  780 LYS cc_start: 0.7818 (pttt) cc_final: 0.7554 (pttm)
REVERT: A  791 PHE cc_start: 0.6383 (t80) cc_final: 0.5957 (t80)
REVERT: F  423 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7735 (m90)
REVERT: F  446 LEU cc_start: 0.8332 (mt) cc_final: 0.8010 (mt)
REVERT: F  573 HIS cc_start: 0.7826 (m-70) cc_final: 0.7583 (m-70)
REVERT: F  581 MET cc_start: 0.8181 (tpp) cc_final: 0.7769 (tpp)
REVERT: F  666 PHE cc_start: 0.8729 (m-80) cc_final: 0.8420 (m-10)
REVERT: F  759 ILE cc_start: 0.7315 (mm) cc_final: 0.7032 (mm)
REVERT: F  786 ASP cc_start: 0.2937 (p0) cc_final: 0.1396 (t0)
REVERT: F  800 MET cc_start: 0.2180 (tpt) cc_final: 0.1912 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1687
  time to fit residues: 36.9476
Evaluate side-chains
  128 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6582
moved from start:          0.7521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6693  Z= 0.173
  Angle     :  0.675  10.227   9062  Z= 0.329
  Chirality :  0.045   0.257   1084
  Planarity :  0.004   0.056   1137
  Dihedral  :  4.683  22.822    864
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.58 %
    Favored  : 98.29 %
  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: -2.78 (0.29), residues: 807
  helix: -2.57 (0.29), residues: 260
  sheet: -2.81 (0.41), residues: 158
  loop : -0.62 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.005   TRP A 803 
 HIS   0.008   0.001   HIS F 598 
 PHE   0.016   0.002   PHE A 728 
 TYR   0.011   0.001   TYR F 692 
 ARG   0.003   0.000   ARG A 734 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8348 (pt0) cc_final: 0.8029 (pt0)
REVERT: A  434 MET cc_start: 0.8772 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  436 SER cc_start: 0.8950 (m) cc_final: 0.8572 (t)
REVERT: A  506 LYS cc_start: 0.9422 (pttm) cc_final: 0.9199 (mmmt)
REVERT: A  520 GLU cc_start: 0.7997 (tt0) cc_final: 0.7789 (tt0)
REVERT: A  576 ASN cc_start: 0.9462 (m-40) cc_final: 0.9123 (m-40)
REVERT: A  639 HIS cc_start: 0.8841 (t-90) cc_final: 0.8603 (p-80)
REVERT: A  686 LYS cc_start: 0.7492 (mtmm) cc_final: 0.7154 (tptm)
REVERT: A  687 LEU cc_start: 0.8792 (mt) cc_final: 0.8428 (mt)
REVERT: A  760 GLU cc_start: 0.8294 (pt0) cc_final: 0.8071 (pt0)
REVERT: A  780 LYS cc_start: 0.7843 (pttt) cc_final: 0.7557 (pttm)
REVERT: A  791 PHE cc_start: 0.6454 (t80) cc_final: 0.5958 (t80)
REVERT: F  446 LEU cc_start: 0.8260 (mt) cc_final: 0.7941 (mt)
REVERT: F  513 LEU cc_start: 0.6965 (mt) cc_final: 0.6683 (mt)
REVERT: F  573 HIS cc_start: 0.7759 (m-70) cc_final: 0.7546 (m-70)
REVERT: F  581 MET cc_start: 0.8207 (tpp) cc_final: 0.7749 (tpp)
REVERT: F  666 PHE cc_start: 0.8762 (m-80) cc_final: 0.8428 (m-10)
REVERT: F  786 ASP cc_start: 0.2716 (p0) cc_final: 0.1297 (t70)
REVERT: F  800 MET cc_start: 0.2632 (tpt) cc_final: 0.2094 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1710
  time to fit residues: 37.0822
Evaluate side-chains
  120 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 647 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.7819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6693  Z= 0.194
  Angle     :  0.684   9.973   9062  Z= 0.337
  Chirality :  0.046   0.273   1084
  Planarity :  0.005   0.045   1137
  Dihedral  :  4.741  22.671    864
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.79 %
    Favored  : 99.08 %
  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: -2.62 (0.30), residues: 807
  helix: -2.55 (0.29), residues: 255
  sheet: -2.74 (0.41), residues: 158
  loop : -0.47 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.006   TRP F 645 
 HIS   0.005   0.001   HIS A 694 
 PHE   0.024   0.002   PHE F 500 
 TYR   0.038   0.002   TYR F 511 
 ARG   0.013   0.001   ARG F 686 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8363 (pt0) cc_final: 0.7989 (pt0)
REVERT: A  434 MET cc_start: 0.8869 (mmm) cc_final: 0.8665 (mmm)
REVERT: A  436 SER cc_start: 0.8936 (m) cc_final: 0.8549 (t)
REVERT: A  520 GLU cc_start: 0.8051 (tt0) cc_final: 0.7844 (tt0)
REVERT: A  576 ASN cc_start: 0.9439 (m-40) cc_final: 0.9046 (m-40)
REVERT: A  595 GLU cc_start: 0.8964 (mp0) cc_final: 0.8710 (mp0)
REVERT: A  639 HIS cc_start: 0.8837 (t-90) cc_final: 0.8586 (p-80)
REVERT: A  686 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7198 (tptm)
REVERT: A  687 LEU cc_start: 0.8770 (mt) cc_final: 0.8403 (mt)
REVERT: A  780 LYS cc_start: 0.7938 (pttt) cc_final: 0.7686 (pttm)
REVERT: A  791 PHE cc_start: 0.6535 (t80) cc_final: 0.6088 (t80)
REVERT: F  446 LEU cc_start: 0.8311 (mt) cc_final: 0.8001 (mt)
REVERT: F  496 LEU cc_start: 0.8448 (tp) cc_final: 0.7483 (tp)
REVERT: F  513 LEU cc_start: 0.6903 (mt) cc_final: 0.6562 (mt)
REVERT: F  581 MET cc_start: 0.8254 (tpp) cc_final: 0.7761 (tpp)
REVERT: F  666 PHE cc_start: 0.8630 (m-80) cc_final: 0.7051 (m-10)
REVERT: F  786 ASP cc_start: 0.2765 (p0) cc_final: 0.1300 (t70)
REVERT: F  800 MET cc_start: 0.2826 (tpt) cc_final: 0.2209 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1557
  time to fit residues: 33.0555
Evaluate side-chains
  115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 409 ASN
** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 573 HIS
** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.8865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6693  Z= 0.411
  Angle     :  0.966  12.553   9062  Z= 0.474
  Chirality :  0.054   0.343   1084
  Planarity :  0.007   0.061   1137
  Dihedral  :  5.808  22.523    864
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 29.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.05 %
    Favored  : 98.82 %
  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: -3.20 (0.28), residues: 807
  helix: -3.06 (0.26), residues: 252
  sheet: -3.03 (0.40), residues: 157
  loop : -0.84 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.006   TRP A 803 
 HIS   0.019   0.002   HIS F 598 
 PHE   0.034   0.004   PHE F 764 
 TYR   0.034   0.003   TYR F 511 
 ARG   0.016   0.002   ARG A 719 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8313 (pt0) cc_final: 0.7969 (pt0)
REVERT: A  434 MET cc_start: 0.8892 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  436 SER cc_start: 0.9023 (m) cc_final: 0.8703 (t)
REVERT: A  504 ASP cc_start: 0.8539 (t70) cc_final: 0.8187 (p0)
REVERT: A  576 ASN cc_start: 0.9420 (m-40) cc_final: 0.9160 (m-40)
REVERT: A  686 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7574 (tptm)
REVERT: F  472 LEU cc_start: 0.9319 (tp) cc_final: 0.9083 (tp)
REVERT: F  513 LEU cc_start: 0.6789 (mt) cc_final: 0.6407 (mt)
REVERT: F  581 MET cc_start: 0.8173 (tpp) cc_final: 0.7666 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1625
  time to fit residues: 33.3814
Evaluate side-chains
  107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 636 GLN
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.8957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6693  Z= 0.244
  Angle     :  0.760  11.134   9062  Z= 0.370
  Chirality :  0.049   0.292   1084
  Planarity :  0.005   0.049   1137
  Dihedral  :  5.469  21.446    864
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 19.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.79 %
    Favored  : 99.08 %
  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: -3.09 (0.29), residues: 807
  helix: -2.94 (0.27), residues: 254
  sheet: -2.74 (0.41), residues: 156
  loop : -0.91 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.004   TRP F 645 
 HIS   0.007   0.001   HIS F 598 
 PHE   0.019   0.002   PHE F 667 
 TYR   0.032   0.003   TYR F 511 
 ARG   0.009   0.001   ARG F 686 

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.8312 (pt0) cc_final: 0.7968 (pt0)
REVERT: A  436 SER cc_start: 0.8904 (m) cc_final: 0.8588 (t)
REVERT: A  520 GLU cc_start: 0.8273 (tt0) cc_final: 0.7977 (tt0)
REVERT: A  668 TYR cc_start: 0.7724 (m-80) cc_final: 0.7244 (m-80)
REVERT: A  687 LEU cc_start: 0.8889 (mt) cc_final: 0.8617 (mt)
REVERT: A  713 LEU cc_start: 0.8771 (tp) cc_final: 0.7913 (pp)
REVERT: F  446 LEU cc_start: 0.8488 (mt) cc_final: 0.8256 (mt)
REVERT: F  456 ASN cc_start: 0.7660 (m-40) cc_final: 0.7231 (p0)
REVERT: F  513 LEU cc_start: 0.6944 (mt) cc_final: 0.6658 (mt)
REVERT: F  528 ASP cc_start: 0.5884 (m-30) cc_final: 0.5226 (p0)
REVERT: F  581 MET cc_start: 0.8276 (tpp) cc_final: 0.7787 (tpp)
REVERT: F  800 MET cc_start: 0.4313 (tmm) cc_final: 0.2132 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1572
  time to fit residues: 34.0255
Evaluate side-chains
  119 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 3 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
F 404 ASN
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.122821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.106970 restraints weight = 27129.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.108151 restraints weight = 19843.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.109107 restraints weight = 14288.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.9109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6693  Z= 0.201
  Angle     :  0.725  10.721   9062  Z= 0.354
  Chirality :  0.047   0.282   1084
  Planarity :  0.005   0.052   1137
  Dihedral  :  5.206  21.241    864
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.26 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.29), residues: 807
  helix: -2.86 (0.28), residues: 248
  sheet: -2.70 (0.41), residues: 156
  loop : -0.70 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.006   TRP A 803 
 HIS   0.007   0.001   HIS A 694 
 PHE   0.031   0.002   PHE A 433 
 TYR   0.028   0.002   TYR F 511 
 ARG   0.009   0.001   ARG F 686 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1988.52 seconds
wall clock time: 37 minutes 18.67 seconds (2238.67 seconds total)