Starting phenix.real_space_refine
on Tue Sep 24 03:04:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2024/8drn_27678.cif"
  }
  resolution = 4.12
  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=   0.001 sd=   0.045
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.50, per 1000 atoms: 0.84
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (107.944, 76.504, 88.032, 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: 1.50
  Conformation dependent library (CDL) restraints added in 916.1 milliseconds
  

  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, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
      removed outlier: 3.507A  pdb=" N   TRP A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 445
      removed outlier: 3.723A  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: 3.911A  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: 3.509A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS A 637 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
      removed outlier: 3.627A  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: 3.770A  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
      removed outlier: 3.547A  pdb=" N   TRP F 409 " --> pdb=" O   LEU F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 437 through 443
      removed outlier: 3.921A  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: 3.833A  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: 3.541A  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: 3.832A  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: 3.816A  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: 6.638A  pdb=" N   LEU A 428 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   LYS A 452 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LEU A 430 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   GLU A 454 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   LEU A 432 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
      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: 7.701A  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: 7.282A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.843A  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: 6.819A  pdb=" N   LEU A 736 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      removed outlier: 6.687A  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: 7.013A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.433A  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: 7.975A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 7.362A  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: 7.349A  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: 6.474A  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: 6.681A  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

    142 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1885
        1.33 -     1.46: 912
        1.46 -     1.58: 3861
        1.58 -     1.70: 1
        1.70 -     1.82: 34
  Bond restraints: 6693
  Sorted by residual:
  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 8.95e+00
  bond pdb=" CA  HIS F 573 "
       pdb=" CB  HIS F 573 "
    ideal  model  delta    sigma   weight residual
    1.526  1.564 -0.037 1.53e-02 4.27e+03 6.00e+00
  bond pdb=" N   ASP A 444 "
       pdb=" CA  ASP A 444 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.28e-02 6.10e+03 5.91e+00
  bond pdb=" N   GLN A 570 "
       pdb=" CA  GLN A 570 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.031 1.37e-02 5.33e+03 4.97e+00
  bond pdb=" N   GLY F 523 "
       pdb=" CA  GLY F 523 "
    ideal  model  delta    sigma   weight residual
    1.449  1.480 -0.031 1.45e-02 4.76e+03 4.43e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 8760
        2.34 -     4.69: 246
        4.69 -     7.03: 35
        7.03 -     9.38: 17
        9.38 -    11.72: 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  124.42  -11.72 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  121.61   -7.51 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  121.59   -7.49 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  MET F 432 "
        pdb=" CB  MET F 432 "
        pdb=" CG  MET F 432 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  ... (remaining 9057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 3644
       17.88 -    35.76: 399
       35.76 -    53.64: 95
       53.64 -    71.52: 13
       71.52 -    89.39: 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  157.53   22.47     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  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLU A 429 "
           pdb=" C   GLU A 429 "
           pdb=" N   LEU A 430 "
           pdb=" CA  LEU A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1027
       0.098 -    0.195: 55
       0.195 -    0.293: 1
       0.293 -    0.390: 0
       0.390 -    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 5.94e+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 1.65e+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 7.28e-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   2.93e-02 2.15e+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 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 475 "   -0.001 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   2.12e-02 8.95e+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 5.72e+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: 1498
        2.79 -     3.32: 6482
        3.32 -     3.85: 11414
        3.85 -     4.37: 14444
        4.37 -     4.90: 22664
  Nonbonded interactions: 56502
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 689 "
            pdb=" OG  SER F 691 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   LEU A 405 "
            pdb=" ND2 ASN A 409 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   ARG A 419 "
            pdb=" NH1 ARG A 419 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OE1 GLU A 429 "
            pdb=" NZ  LYS A 452 "
     model   vdw
     2.297 3.120
  ... (remaining 56497 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:             3.370
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.950
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
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      :  0.004   0.102   6693  Z= 0.285
  Angle     :  0.981  11.724   9062  Z= 0.510
  Chirality :  0.050   0.488   1084
  Planarity :  0.005   0.041   1137
  Dihedral  : 15.665  89.395   2580
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.58 %
    Favored  : 78.16 %
  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: -2.79 (0.28), residues: 248
  sheet: -2.18 (0.53), residues: 113
  loop : -0.96 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.006   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   0.006   0.001   ARG A 419 

*********************** 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
  282 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 280
  time to evaluate  : 0.865 
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: A  404 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7149 (tm-30)
REVERT: A  414 ASP cc_start: 0.9263 (m-30) cc_final: 0.9055 (m-30)
REVERT: A  454 GLU cc_start: 0.8379 (tt0) cc_final: 0.7941 (tm-30)
REVERT: A  473 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8287 (tt0)
REVERT: A  479 THR cc_start: 0.8730 (m) cc_final: 0.8258 (p)
REVERT: A  518 LEU cc_start: 0.8894 (tp) cc_final: 0.8160 (tp)
REVERT: A  547 LYS cc_start: 0.7844 (mttp) cc_final: 0.7594 (mptt)
REVERT: A  601 CYS cc_start: 0.8010 (t) cc_final: 0.7640 (m)
REVERT: A  624 ASN cc_start: 0.8450 (m-40) cc_final: 0.7962 (m110)
REVERT: A  682 PHE cc_start: 0.8170 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  694 HIS cc_start: 0.8789 (m170) cc_final: 0.8582 (m170)
REVERT: A  801 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7229 (tmt170)
REVERT: A  803 TRP cc_start: 0.8431 (m100) cc_final: 0.8221 (m100)
REVERT: F  421 ASN cc_start: 0.7637 (p0) cc_final: 0.7374 (p0)
REVERT: F  486 LEU cc_start: 0.7943 (mt) cc_final: 0.7508 (tt)
REVERT: F  503 MET cc_start: 0.7456 (mmt) cc_final: 0.6148 (tpp)
REVERT: F  511 TYR cc_start: 0.7218 (m-80) cc_final: 0.6135 (m-80)
REVERT: F  518 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6826 (mt-10)
REVERT: F  567 LEU cc_start: 0.8318 (tp) cc_final: 0.7984 (tp)
REVERT: F  588 MET cc_start: 0.7919 (mmp) cc_final: 0.7575 (mmm)
REVERT: F  633 PHE cc_start: 0.8834 (m-80) cc_final: 0.8073 (m-80)
REVERT: F  642 LEU cc_start: 0.7101 (tp) cc_final: 0.6216 (tt)
REVERT: F  649 ILE cc_start: 0.8160 (mt) cc_final: 0.7051 (mm)
REVERT: F  735 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7454 (mtmm)
REVERT: F  756 TYR cc_start: 0.7701 (t80) cc_final: 0.6893 (t80)
REVERT: F  764 PHE cc_start: 0.7230 (m-10) cc_final: 0.6911 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 282
  average time/residue: 0.2175
  time to fit residues: 77.5333
Evaluate side-chains
  181 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0030
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 624 ASN
A 650 HIS
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 706 GLN
F 799 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6693  Z= 0.317
  Angle     :  0.788  10.398   9062  Z= 0.390
  Chirality :  0.049   0.302   1084
  Planarity :  0.006   0.073   1137
  Dihedral  :  5.368  19.308    864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.42 %
    Favored  : 96.45 %
  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: -2.50 (0.29), residues: 807
  helix: -2.46 (0.29), residues: 249
  sheet: -2.47 (0.48), residues: 132
  loop : -0.70 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP F 645 
 HIS   0.007   0.001   HIS F 598 
 PHE   0.025   0.003   PHE A 433 
 TYR   0.025   0.003   TYR F 511 
 ARG   0.006   0.001   ARG F 514 

*********************** 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
  206 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  404 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: A  410 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8334 (mm-30)
REVERT: A  429 GLU cc_start: 0.6801 (mp0) cc_final: 0.6460 (mp0)
REVERT: A  475 TRP cc_start: 0.7843 (m-10) cc_final: 0.7348 (m-10)
REVERT: A  518 LEU cc_start: 0.8542 (tp) cc_final: 0.8170 (tp)
REVERT: A  557 LYS cc_start: 0.8408 (tptt) cc_final: 0.7552 (tmtt)
REVERT: A  645 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7640 (mtpp)
REVERT: A  682 PHE cc_start: 0.8221 (m-80) cc_final: 0.7933 (m-80)
REVERT: A  752 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6364 (mt-10)
REVERT: A  801 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7316 (tmt170)
REVERT: F  432 MET cc_start: 0.7954 (mtm) cc_final: 0.7555 (tpt)
REVERT: F  452 GLU cc_start: 0.8343 (tp30) cc_final: 0.7461 (tp30)
REVERT: F  501 ASP cc_start: 0.8111 (t0) cc_final: 0.7799 (m-30)
REVERT: F  503 MET cc_start: 0.6781 (mmt) cc_final: 0.6533 (tpp)
REVERT: F  550 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7412 (mttm)
REVERT: F  570 MET cc_start: 0.8016 (mmm) cc_final: 0.7571 (mmm)
REVERT: F  573 HIS cc_start: 0.7845 (m170) cc_final: 0.7449 (m170)
REVERT: F  581 MET cc_start: 0.6917 (tpt) cc_final: 0.6663 (tpt)
REVERT: F  588 MET cc_start: 0.8222 (mmp) cc_final: 0.7572 (mmm)
REVERT: F  633 PHE cc_start: 0.8526 (m-80) cc_final: 0.7891 (m-80)
REVERT: F  647 ASN cc_start: 0.6893 (t0) cc_final: 0.6105 (t0)
REVERT: F  726 TYR cc_start: 0.6698 (m-80) cc_final: 0.6455 (m-80)
REVERT: F  771 LEU cc_start: 0.8651 (mm) cc_final: 0.8397 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1943
  time to fit residues: 52.6379
Evaluate side-chains
  145 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 60 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 431 HIS
A 576 ASN
A 657 GLN
A 711 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 799 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.4842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6693  Z= 0.206
  Angle     :  0.690   8.972   9062  Z= 0.342
  Chirality :  0.047   0.252   1084
  Planarity :  0.004   0.033   1137
  Dihedral  :  5.096  17.416    864
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 19.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.55 %
    Favored  : 96.18 %
  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: -2.50 (0.29), residues: 807
  helix: -2.28 (0.30), residues: 250
  sheet: -2.63 (0.47), residues: 125
  loop : -0.80 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP F 645 
 HIS   0.006   0.001   HIS A 694 
 PHE   0.015   0.002   PHE F 666 
 TYR   0.022   0.002   TYR F 511 
 ARG   0.003   0.000   ARG F 664 

*********************** 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
  185 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.802 
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: A  410 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8182 (mm-30)
REVERT: A  473 GLU cc_start: 0.8699 (tt0) cc_final: 0.8490 (tt0)
REVERT: A  518 LEU cc_start: 0.8568 (tp) cc_final: 0.8338 (tp)
REVERT: A  520 GLU cc_start: 0.8347 (mp0) cc_final: 0.8101 (mp0)
REVERT: A  647 TRP cc_start: 0.6396 (p90) cc_final: 0.5614 (p90)
REVERT: A  665 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7166 (tm-30)
REVERT: A  694 HIS cc_start: 0.8739 (m170) cc_final: 0.8500 (m170)
REVERT: A  799 LYS cc_start: 0.8335 (pttm) cc_final: 0.8069 (ptpt)
REVERT: A  801 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7287 (tmt170)
REVERT: F  432 MET cc_start: 0.7971 (mtm) cc_final: 0.7761 (mtp)
REVERT: F  452 GLU cc_start: 0.8489 (tp30) cc_final: 0.8097 (tp30)
REVERT: F  503 MET cc_start: 0.6764 (mmt) cc_final: 0.6436 (tpp)
REVERT: F  550 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7691 (mttm)
REVERT: F  570 MET cc_start: 0.8061 (mmm) cc_final: 0.7540 (mmm)
REVERT: F  573 HIS cc_start: 0.7775 (m170) cc_final: 0.7279 (m170)
REVERT: F  588 MET cc_start: 0.8446 (mmp) cc_final: 0.7916 (mmm)
REVERT: F  594 LEU cc_start: 0.9323 (tp) cc_final: 0.8440 (tp)
REVERT: F  595 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8003 (mm-30)
REVERT: F  616 GLU cc_start: 0.8617 (pt0) cc_final: 0.7977 (pp20)
REVERT: F  617 LEU cc_start: 0.8615 (tt) cc_final: 0.8230 (tt)
REVERT: F  644 LEU cc_start: 0.9009 (mt) cc_final: 0.8738 (mt)
REVERT: F  647 ASN cc_start: 0.7131 (t0) cc_final: 0.6390 (t0)
REVERT: F  687 TYR cc_start: 0.8351 (t80) cc_final: 0.7947 (t80)
REVERT: F  706 GLN cc_start: 0.6384 (tp-100) cc_final: 0.6169 (tp-100)
REVERT: F  726 TYR cc_start: 0.6364 (m-80) cc_final: 0.6125 (m-80)
REVERT: F  764 PHE cc_start: 0.7470 (m-10) cc_final: 0.6998 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1609
  time to fit residues: 41.2169
Evaluate side-chains
  141 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 20 optimal weight:    0.1980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 718 ASN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.5354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6693  Z= 0.215
  Angle     :  0.663  10.912   9062  Z= 0.324
  Chirality :  0.046   0.252   1084
  Planarity :  0.005   0.050   1137
  Dihedral  :  4.842  15.759    864
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 21.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  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: -2.42 (0.30), residues: 807
  helix: -2.25 (0.30), residues: 262
  sheet: -2.51 (0.44), residues: 142
  loop : -0.58 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.004   TRP A 647 
 HIS   0.003   0.001   HIS A 694 
 PHE   0.014   0.002   PHE A 433 
 TYR   0.031   0.002   TYR A 648 
 ARG   0.003   0.000   ARG A 762 

*********************** 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
  174 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8400 (mm-30)
REVERT: A  473 GLU cc_start: 0.8706 (tt0) cc_final: 0.8338 (tt0)
REVERT: A  557 LYS cc_start: 0.8078 (tptt) cc_final: 0.7085 (tmtt)
REVERT: A  624 ASN cc_start: 0.8123 (m-40) cc_final: 0.7757 (m-40)
REVERT: A  647 TRP cc_start: 0.6227 (p90) cc_final: 0.6002 (p90)
REVERT: A  665 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7150 (tm-30)
REVERT: A  666 ARG cc_start: 0.7868 (mtp85) cc_final: 0.6853 (mtm110)
REVERT: A  682 PHE cc_start: 0.8322 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  703 ASP cc_start: 0.8357 (m-30) cc_final: 0.7923 (p0)
REVERT: A  773 LEU cc_start: 0.9176 (tp) cc_final: 0.8861 (tp)
REVERT: A  801 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7259 (tmt170)
REVERT: F  432 MET cc_start: 0.7764 (mtm) cc_final: 0.7280 (tpt)
REVERT: F  452 GLU cc_start: 0.8322 (tp30) cc_final: 0.7929 (tp30)
REVERT: F  503 MET cc_start: 0.6847 (mmt) cc_final: 0.6292 (tpp)
REVERT: F  570 MET cc_start: 0.8101 (mmm) cc_final: 0.7699 (mmm)
REVERT: F  581 MET cc_start: 0.6687 (tpt) cc_final: 0.6440 (tpt)
REVERT: F  588 MET cc_start: 0.8369 (mmp) cc_final: 0.7787 (mmm)
REVERT: F  594 LEU cc_start: 0.9323 (tp) cc_final: 0.8503 (tp)
REVERT: F  595 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8120 (mm-30)
REVERT: F  616 GLU cc_start: 0.8556 (pt0) cc_final: 0.8084 (pp20)
REVERT: F  617 LEU cc_start: 0.8620 (tt) cc_final: 0.8237 (tt)
REVERT: F  670 ASN cc_start: 0.6740 (t0) cc_final: 0.5916 (t0)
REVERT: F  673 GLU cc_start: 0.7092 (tp30) cc_final: 0.6866 (pm20)
REVERT: F  726 TYR cc_start: 0.6532 (m-80) cc_final: 0.6328 (m-80)
REVERT: F  764 PHE cc_start: 0.7645 (m-10) cc_final: 0.7077 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1746
  time to fit residues: 40.6436
Evaluate side-chains
  137 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 416 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.5839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6693  Z= 0.296
  Angle     :  0.707   8.441   9062  Z= 0.350
  Chirality :  0.047   0.210   1084
  Planarity :  0.005   0.045   1137
  Dihedral  :  4.997  19.356    864
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 23.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  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: -2.57 (0.29), residues: 807
  helix: -2.24 (0.30), residues: 267
  sheet: -2.74 (0.43), residues: 138
  loop : -0.71 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP A 647 
 HIS   0.004   0.001   HIS F 598 
 PHE   0.018   0.002   PHE F 666 
 TYR   0.027   0.003   TYR F 687 
 ARG   0.004   0.001   ARG A 666 

*********************** 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
  165 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 GLU cc_start: 0.8641 (tt0) cc_final: 0.8428 (tt0)
REVERT: A  520 GLU cc_start: 0.8283 (mp0) cc_final: 0.8078 (mp0)
REVERT: A  557 LYS cc_start: 0.8090 (tptt) cc_final: 0.7083 (tmtt)
REVERT: A  624 ASN cc_start: 0.8419 (m-40) cc_final: 0.8031 (m-40)
REVERT: A  665 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7165 (tm-30)
REVERT: A  666 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7421 (mtm180)
REVERT: A  740 ASN cc_start: 0.8761 (t0) cc_final: 0.8488 (t0)
REVERT: A  801 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7330 (tmt170)
REVERT: F  432 MET cc_start: 0.7961 (mtm) cc_final: 0.7392 (tpt)
REVERT: F  451 LEU cc_start: 0.9260 (mt) cc_final: 0.9029 (mt)
REVERT: F  452 GLU cc_start: 0.8440 (tp30) cc_final: 0.7954 (mm-30)
REVERT: F  486 LEU cc_start: 0.7366 (mt) cc_final: 0.7147 (mt)
REVERT: F  503 MET cc_start: 0.6981 (mmt) cc_final: 0.6273 (tpp)
REVERT: F  513 LEU cc_start: 0.8080 (mt) cc_final: 0.7701 (mt)
REVERT: F  570 MET cc_start: 0.8021 (mmm) cc_final: 0.7531 (mmm)
REVERT: F  581 MET cc_start: 0.6954 (tpt) cc_final: 0.6607 (tpt)
REVERT: F  588 MET cc_start: 0.8404 (mmp) cc_final: 0.7927 (mmm)
REVERT: F  594 LEU cc_start: 0.9369 (tp) cc_final: 0.8974 (tp)
REVERT: F  595 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8256 (mm-30)
REVERT: F  616 GLU cc_start: 0.8653 (pt0) cc_final: 0.8385 (pt0)
REVERT: F  618 ASP cc_start: 0.7649 (t0) cc_final: 0.6839 (t70)
REVERT: F  764 PHE cc_start: 0.7684 (m-10) cc_final: 0.6988 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1611
  time to fit residues: 36.4343
Evaluate side-chains
  131 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 15 optimal weight:    0.2980
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0270
   chunk 40 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.6012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6693  Z= 0.182
  Angle     :  0.658  10.570   9062  Z= 0.319
  Chirality :  0.046   0.202   1084
  Planarity :  0.004   0.036   1137
  Dihedral  :  4.768  15.900    864
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 21.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    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: -2.45 (0.30), residues: 807
  helix: -2.28 (0.30), residues: 262
  sheet: -2.48 (0.43), residues: 146
  loop : -0.58 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.005   TRP A 647 
 HIS   0.008   0.001   HIS F 573 
 PHE   0.017   0.002   PHE F 666 
 TYR   0.026   0.002   TYR A 648 
 ARG   0.003   0.000   ARG A 671 

*********************** 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
  170 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.8614 (tp) cc_final: 0.8368 (tp)
REVERT: A  520 GLU cc_start: 0.8367 (mp0) cc_final: 0.8130 (mp0)
REVERT: A  557 LYS cc_start: 0.8019 (tptt) cc_final: 0.7010 (tmtt)
REVERT: A  624 ASN cc_start: 0.8422 (m-40) cc_final: 0.7993 (m-40)
REVERT: A  645 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7785 (ptpt)
REVERT: A  647 TRP cc_start: 0.6458 (p90) cc_final: 0.5806 (p90)
REVERT: A  665 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6869 (tm-30)
REVERT: A  666 ARG cc_start: 0.7880 (mtp85) cc_final: 0.6964 (mtm110)
REVERT: A  801 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7342 (tmt170)
REVERT: F  486 LEU cc_start: 0.7334 (mt) cc_final: 0.7085 (mt)
REVERT: F  503 MET cc_start: 0.6994 (mmt) cc_final: 0.6228 (tpp)
REVERT: F  550 LYS cc_start: 0.8394 (mttt) cc_final: 0.7778 (mmtt)
REVERT: F  570 MET cc_start: 0.8001 (mmm) cc_final: 0.7561 (mmm)
REVERT: F  581 MET cc_start: 0.6933 (tpt) cc_final: 0.6538 (tpt)
REVERT: F  588 MET cc_start: 0.8319 (mmp) cc_final: 0.7848 (mmm)
REVERT: F  594 LEU cc_start: 0.9335 (tp) cc_final: 0.8980 (tp)
REVERT: F  595 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8258 (mm-30)
REVERT: F  616 GLU cc_start: 0.8514 (pt0) cc_final: 0.8237 (pt0)
REVERT: F  618 ASP cc_start: 0.7741 (t0) cc_final: 0.6870 (t70)
REVERT: F  692 TYR cc_start: 0.8106 (m-80) cc_final: 0.7879 (m-80)
REVERT: F  764 PHE cc_start: 0.7571 (m-10) cc_final: 0.6887 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1806
  time to fit residues: 40.9545
Evaluate side-chains
  131 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 576 ASN
A 608 HIS
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 468 ASN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.6453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6693  Z= 0.302
  Angle     :  0.733   9.500   9062  Z= 0.356
  Chirality :  0.049   0.266   1084
  Planarity :  0.005   0.042   1137
  Dihedral  :  5.037  19.671    864
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 24.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    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: -2.58 (0.29), residues: 807
  helix: -2.25 (0.30), residues: 264
  sheet: -2.68 (0.43), residues: 138
  loop : -0.76 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.004   TRP A 647 
 HIS   0.005   0.001   HIS F 678 
 PHE   0.016   0.002   PHE F 666 
 TYR   0.018   0.002   TYR F 726 
 ARG   0.004   0.000   ARG F 425 

*********************** 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
  156 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 MET cc_start: 0.8807 (mmm) cc_final: 0.8595 (mmm)
REVERT: A  518 LEU cc_start: 0.8556 (tp) cc_final: 0.8347 (tp)
REVERT: A  520 GLU cc_start: 0.8291 (mp0) cc_final: 0.7968 (mp0)
REVERT: A  557 LYS cc_start: 0.8012 (tptt) cc_final: 0.6990 (tmtt)
REVERT: A  624 ASN cc_start: 0.8493 (m-40) cc_final: 0.8103 (m-40)
REVERT: A  645 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7592 (mtmt)
REVERT: A  647 TRP cc_start: 0.6992 (p90) cc_final: 0.5852 (p90)
REVERT: A  665 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6880 (tm-30)
REVERT: A  666 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7237 (mtm180)
REVERT: A  694 HIS cc_start: 0.8661 (m170) cc_final: 0.8406 (m170)
REVERT: A  801 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7358 (tmt170)
REVERT: F  452 GLU cc_start: 0.8404 (tp30) cc_final: 0.8036 (tp30)
REVERT: F  486 LEU cc_start: 0.7514 (mt) cc_final: 0.7206 (mt)
REVERT: F  503 MET cc_start: 0.7249 (mmt) cc_final: 0.6263 (tpp)
REVERT: F  550 LYS cc_start: 0.8352 (mttt) cc_final: 0.7850 (mmtt)
REVERT: F  570 MET cc_start: 0.8145 (mmm) cc_final: 0.7887 (mmm)
REVERT: F  581 MET cc_start: 0.7139 (tpt) cc_final: 0.6649 (tpt)
REVERT: F  588 MET cc_start: 0.8360 (mmp) cc_final: 0.7828 (mmm)
REVERT: F  594 LEU cc_start: 0.9350 (tp) cc_final: 0.8930 (tp)
REVERT: F  595 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8343 (mm-30)
REVERT: F  616 GLU cc_start: 0.8611 (pt0) cc_final: 0.8395 (pt0)
REVERT: F  618 ASP cc_start: 0.7870 (t0) cc_final: 0.6947 (t70)
REVERT: F  764 PHE cc_start: 0.7792 (m-10) cc_final: 0.6993 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1672
  time to fit residues: 35.5154
Evaluate side-chains
  119 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0170
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.6554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.097   6693  Z= 0.198
  Angle     :  0.694  11.471   9062  Z= 0.331
  Chirality :  0.047   0.221   1084
  Planarity :  0.004   0.059   1137
  Dihedral  :  4.824  18.803    864
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 20.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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: -2.47 (0.29), residues: 807
  helix: -2.23 (0.31), residues: 258
  sheet: -2.62 (0.42), residues: 144
  loop : -0.62 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 647 
 HIS   0.007   0.001   HIS F 573 
 PHE   0.015   0.002   PHE F 666 
 TYR   0.018   0.002   TYR F 756 
 ARG   0.003   0.000   ARG A 671 

*********************** 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
  168 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.840 
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  473 GLU cc_start: 0.8560 (tt0) cc_final: 0.8342 (tt0)
REVERT: A  520 GLU cc_start: 0.8359 (mp0) cc_final: 0.8021 (mp0)
REVERT: A  557 LYS cc_start: 0.7982 (tptt) cc_final: 0.6938 (tmtt)
REVERT: A  624 ASN cc_start: 0.8335 (m-40) cc_final: 0.7867 (m-40)
REVERT: A  645 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7709 (ptpt)
REVERT: A  647 TRP cc_start: 0.6843 (p90) cc_final: 0.5466 (p90)
REVERT: A  665 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6736 (tm-30)
REVERT: A  694 HIS cc_start: 0.8783 (m170) cc_final: 0.8537 (m170)
REVERT: A  801 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7378 (tmt170)
REVERT: F  486 LEU cc_start: 0.7258 (mt) cc_final: 0.6981 (mt)
REVERT: F  503 MET cc_start: 0.7120 (mmt) cc_final: 0.6152 (tpp)
REVERT: F  570 MET cc_start: 0.8098 (mmm) cc_final: 0.7796 (mmp)
REVERT: F  581 MET cc_start: 0.6958 (tpt) cc_final: 0.6489 (tpt)
REVERT: F  588 MET cc_start: 0.8277 (mmp) cc_final: 0.7772 (mmm)
REVERT: F  594 LEU cc_start: 0.9304 (tp) cc_final: 0.8916 (tp)
REVERT: F  595 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8307 (mm-30)
REVERT: F  616 GLU cc_start: 0.8564 (pt0) cc_final: 0.8345 (pt0)
REVERT: F  618 ASP cc_start: 0.7674 (t0) cc_final: 0.6956 (t70)
REVERT: F  688 LEU cc_start: 0.8748 (tp) cc_final: 0.8418 (tp)
REVERT: F  764 PHE cc_start: 0.7514 (m-10) cc_final: 0.6723 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1825
  time to fit residues: 41.1109
Evaluate side-chains
  126 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 22 optimal weight:    0.4980
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.6773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   6693  Z= 0.220
  Angle     :  0.720  10.740   9062  Z= 0.343
  Chirality :  0.048   0.183   1084
  Planarity :  0.004   0.050   1137
  Dihedral  :  4.827  18.103    864
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.30), residues: 807
  helix: -2.19 (0.31), residues: 250
  sheet: -2.66 (0.42), residues: 148
  loop : -0.46 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 647 
 HIS   0.007   0.001   HIS F 573 
 PHE   0.026   0.002   PHE A 433 
 TYR   0.021   0.002   TYR A 648 
 ARG   0.002   0.000   ARG A 762 

*********************** 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
  168 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 GLU cc_start: 0.8558 (tt0) cc_final: 0.8251 (tt0)
REVERT: A  520 GLU cc_start: 0.8348 (mp0) cc_final: 0.8009 (mp0)
REVERT: A  557 LYS cc_start: 0.7993 (tptt) cc_final: 0.6923 (tmtt)
REVERT: A  645 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7651 (ptpt)
REVERT: A  647 TRP cc_start: 0.7134 (p90) cc_final: 0.5716 (p90)
REVERT: A  665 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: A  801 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7404 (tmt170)
REVERT: F  486 LEU cc_start: 0.7322 (mt) cc_final: 0.7024 (mt)
REVERT: F  503 MET cc_start: 0.7211 (mmt) cc_final: 0.6134 (tpp)
REVERT: F  550 LYS cc_start: 0.8557 (mttt) cc_final: 0.8128 (mmtt)
REVERT: F  570 MET cc_start: 0.8163 (mmm) cc_final: 0.7884 (mmm)
REVERT: F  581 MET cc_start: 0.7082 (tpt) cc_final: 0.6611 (tpt)
REVERT: F  588 MET cc_start: 0.8360 (mmp) cc_final: 0.7885 (mmm)
REVERT: F  594 LEU cc_start: 0.9291 (tp) cc_final: 0.8918 (tp)
REVERT: F  595 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8326 (mm-30)
REVERT: F  616 GLU cc_start: 0.8569 (pt0) cc_final: 0.8355 (pt0)
REVERT: F  618 ASP cc_start: 0.7675 (t0) cc_final: 0.6850 (t70)
REVERT: F  662 LEU cc_start: 0.8976 (tp) cc_final: 0.8636 (mp)
REVERT: F  764 PHE cc_start: 0.7709 (m-10) cc_final: 0.6840 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1641
  time to fit residues: 37.2652
Evaluate side-chains
  120 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 6 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.7078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6693  Z= 0.285
  Angle     :  0.737   9.188   9062  Z= 0.360
  Chirality :  0.048   0.169   1084
  Planarity :  0.005   0.047   1137
  Dihedral  :  4.994  21.093    864
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 23.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.57 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.47 (0.29), residues: 807
  helix: -2.25 (0.30), residues: 256
  sheet: -2.81 (0.41), residues: 141
  loop : -0.57 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 647 
 HIS   0.005   0.001   HIS F 573 
 PHE   0.024   0.002   PHE A 433 
 TYR   0.023   0.003   TYR F 756 
 ARG   0.006   0.001   ARG F 425 

********************** 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
  155 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  505 ILE cc_start: 0.8239 (mt) cc_final: 0.7784 (tp)
REVERT: A  518 LEU cc_start: 0.8559 (tp) cc_final: 0.8331 (tp)
REVERT: A  520 GLU cc_start: 0.8348 (mp0) cc_final: 0.7985 (mp0)
REVERT: A  557 LYS cc_start: 0.7989 (tptt) cc_final: 0.6962 (tmtt)
REVERT: A  647 TRP cc_start: 0.7299 (p90) cc_final: 0.6295 (p90)
REVERT: A  665 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A  801 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7467 (tmt170)
REVERT: F  486 LEU cc_start: 0.7268 (mt) cc_final: 0.7041 (mt)
REVERT: F  503 MET cc_start: 0.7393 (mmt) cc_final: 0.6278 (tpp)
REVERT: F  516 LEU cc_start: 0.8892 (mm) cc_final: 0.8557 (mm)
REVERT: F  570 MET cc_start: 0.8129 (mmm) cc_final: 0.7834 (mmm)
REVERT: F  581 MET cc_start: 0.7149 (tpt) cc_final: 0.6615 (tpt)
REVERT: F  588 MET cc_start: 0.8229 (mmp) cc_final: 0.7811 (mmm)
REVERT: F  594 LEU cc_start: 0.9337 (tp) cc_final: 0.8953 (tp)
REVERT: F  595 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8361 (mm-30)
REVERT: F  616 GLU cc_start: 0.8634 (pt0) cc_final: 0.8423 (pt0)
REVERT: F  618 ASP cc_start: 0.7922 (t0) cc_final: 0.6938 (t70)
REVERT: F  764 PHE cc_start: 0.7779 (m-10) cc_final: 0.7278 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1667
  time to fit residues: 34.9073
Evaluate side-chains
  115 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0970
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 758 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.116353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.098631 restraints weight = 19641.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.100053 restraints weight = 11604.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.102704 restraints weight = 8164.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.7245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6693  Z= 0.219
  Angle     :  0.721   9.917   9062  Z= 0.345
  Chirality :  0.048   0.184   1084
  Planarity :  0.005   0.045   1137
  Dihedral  :  4.957  21.201    864
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 20.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.45 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.30), residues: 807
  helix: -2.22 (0.31), residues: 256
  sheet: -2.63 (0.42), residues: 148
  loop : -0.44 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP A 647 
 HIS   0.004   0.001   HIS A 694 
 PHE   0.024   0.002   PHE A 433 
 TYR   0.015   0.002   TYR A 648 
 ARG   0.007   0.001   ARG F 664 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1950.38 seconds
wall clock time: 35 minutes 48.89 seconds (2148.89 seconds total)