Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Sep 28 09:18:11 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2023/8drn_27678.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2023/8drn_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_2023/8drn_27678.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2023/8drn_27678.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2023/8drn_27678.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/09_2023/8drn_27678.pdb"
  }
  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
    Residue "A GLU  429": "OE1" <-> "OE2"
    Residue "A GLU  473": "OE1" <-> "OE2"
    Residue "A TYR  513": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  611": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  760": "OE1" <-> "OE2"
    Residue "F GLU  471": "OE1" <-> "OE2"
    Residue "F PHE  488": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  520": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  593": "OE1" <-> "OE2"
    Residue "F GLU  602": "OE1" <-> "OE2"
    Residue "F PHE  633": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  667": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  680": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  687": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  697": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  701": "OE1" <-> "OE2"
    Residue "F GLU  724": "OE1" <-> "OE2"
    Residue "F GLU  770": "OE1" <-> "OE2"
    Residue "F GLU  798": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 4.83, per 1000 atoms: 0.73
  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  - 3.50
        Amino acid           : False - 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: 2.52
  Conformation dependent library (CDL) restraints added in 1.1 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, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  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: 1.68

  Time building geometry restraints manager: 2.73 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:
       97.17 -   104.64: 96
      104.64 -   112.12: 3421
      112.12 -   119.59: 2435
      119.59 -   127.06: 3040
      127.06 -   134.54: 70
  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 2.440
  nonbonded pdb=" O   LEU A 405 "
            pdb=" ND2 ASN A 409 "
     model   vdw
     2.285 2.520
  nonbonded pdb=" O   ARG A 419 "
            pdb=" NH1 ARG A 419 "
     model   vdw
     2.291 2.520
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.297 2.440
  nonbonded pdb=" OE1 GLU A 429 "
            pdb=" NZ  LYS A 452 "
     model   vdw
     2.297 2.520
  ... (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
========== 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:             3.500
  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:          14.850
  Check model and map are aligned:         0.110
  Set scattering table:                    0.060
  Process input model:                     22.400
  Find NCS groups from input model:        0.190
  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:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.740
-------------------------------------------------------------------------------
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

*********************** 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  : 0.810 
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
  outliers start: 2
  outliers final: 0
  residues processed: 282
  average time/residue: 0.2152
  time to fit residues: 76.8980
Evaluate side-chains
  172 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0249
-------------------------------------------------------------------------------
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:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0170
   chunk 46 optimal weight:    9.9990
   chunk 72 optimal weight:    0.0270
   overall best weight:    0.7680

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
A 650 HIS
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 706 GLN
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 799 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
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      :  0.004   0.041   6693  Z= 0.253
  Angle     :  0.751  10.174   9062  Z= 0.366
  Chirality :  0.048   0.309   1084
  Planarity :  0.005   0.072   1137
  Dihedral  :  5.313  19.833    864
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 24.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.76 %
    Favored  : 97.11 %
  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: -2.41 (0.30), residues: 239
  sheet: -2.36 (0.50), residues: 117
  loop : -0.90 (0.29), residues: 451

*********************** 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 fitting.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1889
  time to fit residues: 52.5440
Evaluate side-chains
  141 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.750 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9561
-------------------------------------------------------------------------------
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:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 72 optimal weight:    0.4980
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 ASN
A 657 GLN
A 711 GLN
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.4789

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= 0.218
  Angle     :  0.712   8.105   9062  Z= 0.346
  Chirality :  0.048   0.263   1084
  Planarity :  0.004   0.034   1137
  Dihedral  :  5.011  16.164    864
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 23.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    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: -2.49 (0.29), residues: 807
  helix: -2.19 (0.31), residues: 238
  sheet: -2.41 (0.47), residues: 135
  loop : -0.93 (0.29), residues: 434

*********************** 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
  179 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1589
  time to fit residues: 39.1945
Evaluate side-chains
  132 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.775 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0711
-------------------------------------------------------------------------------
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:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0020
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
A 431 HIS
** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.5358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6693  Z= 0.235
  Angle     :  0.686  10.415   9062  Z= 0.335
  Chirality :  0.048   0.275   1084
  Planarity :  0.004   0.050   1137
  Dihedral  :  4.862  15.265    864
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 24.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  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: -2.39 (0.29), residues: 807
  helix: -2.17 (0.30), residues: 254
  sheet: -2.10 (0.48), residues: 135
  loop : -0.85 (0.30), residues: 418

*********************** 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
  160 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1710
  time to fit residues: 37.1942
Evaluate side-chains
  130 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.790 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9941
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0570
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.1902

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
A 576 ASN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.5766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6693  Z= 0.231
  Angle     :  0.680   9.059   9062  Z= 0.333
  Chirality :  0.047   0.184   1084
  Planarity :  0.005   0.056   1137
  Dihedral  :  4.859  17.172    864
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 24.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  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: -2.20 (0.29), residues: 807
  helix: -2.07 (0.31), residues: 244
  sheet: -1.88 (0.48), residues: 140
  loop : -0.77 (0.30), residues: 423

*********************** 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
  156 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1574
  time to fit residues: 34.0982
Evaluate side-chains
  122 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.793 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0936
-------------------------------------------------------------------------------
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:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.6035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6693  Z= 0.210
  Angle     :  0.660  11.249   9062  Z= 0.320
  Chirality :  0.046   0.198   1084
  Planarity :  0.004   0.055   1137
  Dihedral  :  4.790  18.562    864
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -2.11 (0.30), residues: 807
  helix: -1.99 (0.32), residues: 244
  sheet: -1.79 (0.48), residues: 140
  loop : -0.74 (0.30), residues: 423

*********************** 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
  161 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1671
  time to fit residues: 37.4812
Evaluate side-chains
  131 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.989 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4079
-------------------------------------------------------------------------------
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:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 56 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 416 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.6334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6693  Z= 0.253
  Angle     :  0.705  10.666   9062  Z= 0.343
  Chirality :  0.047   0.191   1084
  Planarity :  0.005   0.051   1137
  Dihedral  :  4.869  18.013    864
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 26.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  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: -2.11 (0.30), residues: 807
  helix: -2.11 (0.31), residues: 248
  sheet: -1.71 (0.49), residues: 140
  loop : -0.65 (0.31), residues: 419

*********************** 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
  158 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1706
  time to fit residues: 36.7448
Evaluate side-chains
  120 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.824 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0385
-------------------------------------------------------------------------------
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:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0270
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0.7166
moved from start:          0.6547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6693  Z= 0.218
  Angle     :  0.719  10.170   9062  Z= 0.348
  Chirality :  0.047   0.242   1084
  Planarity :  0.004   0.048   1137
  Dihedral  :  4.884  18.506    864
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 24.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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: -2.13 (0.30), residues: 807
  helix: -2.14 (0.31), residues: 250
  sheet: -1.55 (0.50), residues: 139
  loop : -0.73 (0.31), residues: 418

*********************** 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
  162 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1630
  time to fit residues: 36.3877
Evaluate side-chains
  123 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.804 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1032
-------------------------------------------------------------------------------
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:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 475 HIS
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.6766

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= 0.220
  Angle     :  0.735  10.819   9062  Z= 0.350
  Chirality :  0.046   0.202   1084
  Planarity :  0.004   0.047   1137
  Dihedral  :  4.985  19.819    864
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    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: -2.16 (0.30), residues: 807
  helix: -2.10 (0.31), residues: 250
  sheet: -1.77 (0.48), residues: 144
  loop : -0.69 (0.31), residues: 413

*********************** 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
  155 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1592
  time to fit residues: 34.3720
Evaluate side-chains
  122 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0927
-------------------------------------------------------------------------------
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:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0980
   chunk 73 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 50 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
A 478 HIS
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 758 GLN
F 416 GLN
F 475 HIS
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.6980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6693  Z= 0.197
  Angle     :  0.731  10.736   9062  Z= 0.345
  Chirality :  0.046   0.167   1084
  Planarity :  0.004   0.046   1137
  Dihedral  :  4.840  14.976    864
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 22.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.66 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.30), residues: 807
  helix: -1.91 (0.32), residues: 243
  sheet: -1.76 (0.48), residues: 145
  loop : -0.61 (0.31), residues: 419

********************** 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
  159 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1807
  time to fit residues: 39.3308
Evaluate side-chains
  121 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0838
-------------------------------------------------------------------------------
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:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.116825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.099354 restraints weight = 20633.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.101092 restraints weight = 14067.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.103113 restraints weight = 9428.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.7264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6693  Z= 0.227
  Angle     :  0.722  10.215   9062  Z= 0.353
  Chirality :  0.047   0.179   1084
  Planarity :  0.005   0.045   1137
  Dihedral  :  4.901  16.980    864
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 26.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    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: -2.04 (0.30), residues: 807
  helix: -1.98 (0.32), residues: 232
  sheet: -1.84 (0.49), residues: 141
  loop : -0.67 (0.30), residues: 434
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.16 seconds
wall clock time: 34 minutes 17.88 seconds (2057.88 seconds total)