Starting phenix.real_space_refine
on Wed Sep 17 04:32:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcp_44433/09_2025/9bcp_44433.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      12      5.16       5
     C    2594      2.51       5
     N     779      2.21       5
     O     771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4162
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2008
          Classifications: {'peptide': 304}
          Incomplete info: {'truncation_to_alanine': 136}
          Link IDs: {'PTRANS': 15, 'TRANS': 288}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 471
          Unresolved non-hydrogen angles: 601
          Unresolved non-hydrogen dihedrals: 367
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLU:plan': 20, 'ARG:plan': 12, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 8, 'PHE:plan': 2, 'HIS:plan': 3, 'GLN:plan1': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 275
    Chain: "A"
      Number of atoms: 2091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2091
          Classifications: {'peptide': 314}
          Incomplete info: {'truncation_to_alanine': 137}
          Link IDs: {'PTRANS': 15, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 465
          Unresolved non-hydrogen angles: 584
          Unresolved non-hydrogen dihedrals: 363
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'GLU:plan': 20, 'TRP:plan': 1, 'ARG:plan': 13, 'ASP:plan': 11, 'PHE:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 5}
          Unresolved non-hydrogen planarities: 254
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.45, per 1000 atoms: 0.35
  Number of scatterers: 4162
  At special positions: 0
  Unit cell: (81.3, 112.736, 67.208, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P       6     15.00
     O     771      8.00
     N     779      7.00
     C    2594      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 120.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1170

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      46.9% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 545 through 557
    Processing helix  chain 'B' and resid 587 through 594
      removed outlier: 3.530A  pdb=" N   ASN B 594 " --> pdb=" O   ASP B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 620
      removed outlier: 3.816A  pdb=" N   ILE B 611 " --> pdb=" O   LEU B 607 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASN B 620 " --> pdb=" O   LEU B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.535A  pdb=" N   LYS B 666 " --> pdb=" O   THR B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 676
    Processing helix  chain 'B' and resid 685 through 703
    Processing helix  chain 'B' and resid 715 through 725
    Processing helix  chain 'B' and resid 741 through 751
      removed outlier: 4.321A  pdb=" N   GLY B 745 " --> pdb=" O   LEU B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 773
    Processing helix  chain 'B' and resid 774 through 776
      No H-bonds generated for 'chain 'B' and resid 774 through 776'
    Processing helix  chain 'B' and resid 781 through 809
      removed outlier: 3.962A  pdb=" N   MET B 788 " --> pdb=" O   LEU B 784 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 789 " --> pdb=" O   LEU B 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 558
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.732A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 619
      removed outlier: 3.738A  pdb=" N   PHE A 617 " --> pdb=" O   LYS A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 4.031A  pdb=" N   CYS A 634 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 668
      removed outlier: 3.978A  pdb=" N   LEU A 668 " --> pdb=" O   TYR A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 677
      removed outlier: 3.575A  pdb=" N   LEU A 675 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   MET A 677 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 702
    Processing helix  chain 'A' and resid 715 through 726
    Processing helix  chain 'A' and resid 741 through 752
    Processing helix  chain 'A' and resid 761 through 773
    Processing helix  chain 'A' and resid 780 through 810
      removed outlier: 4.086A  pdb=" N   LEU A 784 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 524 through 527
      removed outlier: 5.771A  pdb=" N   GLU B 581 " --> pdb=" O   PHE B 566 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   PHE B 566 " --> pdb=" O   GLU B 581 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 526
      removed outlier: 3.554A  pdb=" N   CYS A 577 " --> pdb=" O   CYS A 570 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY A 568 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   GLU A 581 " --> pdb=" O   PHE A 566 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   PHE A 566 " --> pdb=" O   GLU A 581 " (cutoff:3.500A)

    206 hydrogen bonds defined for protein.
    609 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: 0.38

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 704
        1.31 -     1.43: 1114
        1.43 -     1.56: 2405
        1.56 -     1.68: 8
        1.68 -     1.81: 18
  Bond restraints: 4249
  Sorted by residual:
  bond pdb=" C4  ATP B1101 "
       pdb=" C5  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.388  1.466 -0.078 1.00e-02 1.00e+04 6.10e+01
  bond pdb=" C5  ATP B1101 "
       pdb=" C6  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.95e+01
  bond pdb=" C8  ATP B1101 "
       pdb=" N7  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.310  1.357 -0.047 1.00e-02 1.00e+04 2.21e+01
  bond pdb=" C1' ATP A1101 "
       pdb=" N9  ATP A1101 "
    ideal  model  delta    sigma   weight residual
    1.459  1.397  0.062 1.40e-02 5.10e+03 1.93e+01
  bond pdb=" C5  ATP B1101 "
       pdb=" N7  ATP B1101 "
    ideal  model  delta    sigma   weight residual
    1.387  1.343  0.044 1.00e-02 1.00e+04 1.91e+01
  ... (remaining 4244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.28: 5814
        5.28 -    10.56: 19
       10.56 -    15.84: 1
       15.84 -    21.12: 3
       21.12 -    26.41: 2
  Bond angle restraints: 5839
  Sorted by residual:
  angle pdb=" PB  ATP A1101 "
        pdb=" O3B ATP A1101 "
        pdb=" PG  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     139.87  113.46   26.41 1.00e+00 1.00e+00 6.97e+02
  angle pdb=" PA  ATP A1101 "
        pdb=" O3A ATP A1101 "
        pdb=" PB  ATP A1101 "
      ideal   model   delta    sigma   weight residual
     136.83  115.13   21.70 1.00e+00 1.00e+00 4.71e+02
  angle pdb=" PB  ATP B1101 "
        pdb=" O3B ATP B1101 "
        pdb=" PG  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     139.87  120.71   19.16 1.00e+00 1.00e+00 3.67e+02
  angle pdb=" PA  ATP B1101 "
        pdb=" O3A ATP B1101 "
        pdb=" PB  ATP B1101 "
      ideal   model   delta    sigma   weight residual
     136.83  118.16   18.67 1.00e+00 1.00e+00 3.48e+02
  angle pdb=" C   GLN A 790 "
        pdb=" CA  GLN A 790 "
        pdb=" CB  GLN A 790 "
      ideal   model   delta    sigma   weight residual
     110.70  129.71  -19.01 1.83e+00 2.99e-01 1.08e+02
  ... (remaining 5834 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 2331
       17.81 -    35.61: 162
       35.61 -    53.42: 41
       53.42 -    71.23: 8
       71.23 -    89.03: 10
  Dihedral angle restraints: 2552
    sinusoidal: 753
      harmonic: 1799
  Sorted by residual:
  dihedral pdb=" C   GLN A 790 "
           pdb=" N   GLN A 790 "
           pdb=" CA  GLN A 790 "
           pdb=" CB  GLN A 790 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.80   16.20     0      2.50e+00 1.60e-01 4.20e+01
  dihedral pdb=" CA  VAL A 706 "
           pdb=" C   VAL A 706 "
           pdb=" N   PHE A 707 "
           pdb=" CA  PHE A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.79   25.21     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  ASP A 600 "
           pdb=" C   ASP A 600 "
           pdb=" N   TRP A 601 "
           pdb=" CA  TRP A 601 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.47   23.53     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 2549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 612
       0.083 -    0.166: 51
       0.166 -    0.249: 3
       0.249 -    0.331: 0
       0.331 -    0.414: 1
  Chirality restraints: 667
  Sorted by residual:
  chirality pdb=" CA  GLN A 790 "
            pdb=" N   GLN A 790 "
            pdb=" C   GLN A 790 "
            pdb=" CB  GLN A 790 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.29e+00
  chirality pdb=" CA  ASN A 633 "
            pdb=" N   ASN A 633 "
            pdb=" C   ASN A 633 "
            pdb=" CB  ASN A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CA  VAL A 532 "
            pdb=" N   VAL A 532 "
            pdb=" C   VAL A 532 "
            pdb=" CB  VAL A 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.88e-01
  ... (remaining 664 not shown)

  Planarity restraints: 780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 531 "   -0.025 2.00e-02 2.50e+03   4.90e-02 2.40e+01
        pdb=" C   LEU A 531 "    0.085 2.00e-02 2.50e+03
        pdb=" O   LEU A 531 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   VAL A 532 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 656 "    0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO A 657 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 657 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 657 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 755 "    0.051 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO A 756 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 756 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 756 "    0.041 5.00e-02 4.00e+02
  ... (remaining 777 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1818
        2.89 -     3.39: 4209
        3.39 -     3.90: 5859
        3.90 -     4.40: 6112
        4.40 -     4.90: 9694
  Nonbonded interactions: 27692
  Sorted by model distance:
  nonbonded pdb=" O   SER A 632 "
            pdb=" OD1 ASN A 633 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" O   ASN B 773 "
            pdb=" OD1 ASN B 773 "
     model   vdw
     2.399 3.040
  nonbonded pdb=" OD1 ASN B 633 "
            pdb=" O1B ATP B1101 "
     model   vdw
     2.405 3.040
  nonbonded pdb=" O   ASP A 572 "
            pdb=" O   ASN A 575 "
     model   vdw
     2.429 3.040
  nonbonded pdb=" O   PHE A 640 "
            pdb=" NH1 ARG A 787 "
     model   vdw
     2.434 3.120
  ... (remaining 27687 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 473 through 478 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 479 through 485 or (resid 486 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 522 through 525 or (resid 526 through 5 \ 
27 and (name N or name CA or name C or name O or name CB )) or resid 528 through \ 
 529 or (resid 530 through 533 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 534 through 535 or (resid 536 through 541 and (name N or name C \ 
A or name C or name O or name CB )) or resid 542 through 545 or (resid 546 throu \ 
gh 559 and (name N or name CA or name C or name O or name CB )) or resid 560 or  \ 
(resid 561 and (name N or name CA or name C or name O or name CB )) or resid 562 \ 
 or (resid 563 through 567 and (name N or name CA or name C or name O or name CB \ 
 )) or (resid 568 through 572 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 573 through 574 or (resid 575 through 580 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 581 through 600 or (resid 601 throug \ 
h 602 and (name N or name CA or name C or name O or name CB )) or resid 603 thro \ 
ugh 606 or (resid 607 through 613 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 614 through 625 or (resid 626 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 627 through 633 or (resid 634 through 637 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 638 through 661  \ 
or (resid 662 through 665 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 666 through 667 or (resid 668 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 669 through 674 or (resid 675 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 676 through 684 or (resid 685 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 686 through 688 or ( \ 
resid 689 through 690 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 691 through 697 or (resid 698 through 699 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 700 through 713 or (resid 714 through 715 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 716 through 719  \ 
or (resid 720 through 722 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 723 through 733 or (resid 734 through 736 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 737 through 742 or (resid 743 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 744 through 750 or (resi \ 
d 751 and (name N or name CA or name C or name O or name CB )) or resid 752 thro \ 
ugh 766 or (resid 767 through 768 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 769 or (resid 770 through 780 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 781 through 786 or (resid 787 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 788 through 808 or (resid 80 \ 
9 and (name N or name CA or name C or name O or name CB )) or resid 1101))
  selection = (chain 'B' and ((resid 473 through 478 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 479 through 530 or (resid 531 through 533 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 534 or (resid 535 through 5 \ 
41 and (name N or name CA or name C or name O or name CB )) or resid 542 through \ 
 546 or (resid 547 through 559 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 560 through 564 or (resid 565 through 567 and (name N or name C \ 
A or name C or name O or name CB )) or resid 568 through 577 or (resid 578 throu \ 
gh 580 and (name N or name CA or name C or name O or name CB )) or resid 581 thr \ 
ough 593 or (resid 594 through 596 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 597 through 599 or (resid 600 through 602 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 603 through 615 or (resid 616 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 617 through 622 \ 
 or (resid 623 and (name N or name CA or name C or name O or name CB )) or resid \ 
 624 or (resid 625 through 626 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 627 through 634 or (resid 635 through 637 and (name N or name C \ 
A or name C or name O or name CB )) or resid 638 or (resid 639 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 644 through 652 \ 
 or (resid 653 through 654 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 655 through 676 or (resid 677 through 679 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 680 through 682 or (resid 683 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 684 through 691 or (res \ 
id 692 and (name N or name CA or name C or name O or name CB )) or resid 693 thr \ 
ough 694 or (resid 695 through 699 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 700 through 703 or (resid 704 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 705 through 711 or (resid 712 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 713 through 727 or (resid 7 \ 
28 and (name N or name CA or name C or name O or name CB )) or resid 729 through \ 
 738 or (resid 739 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 740 through 772 or (resid 773 through 780 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 781 through 784 or (resid 785 through 787 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 788 or (resid 789 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 790 through 799 \ 
 or (resid 800 through 801 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 802 through 1101))
}

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:             1.120
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.020
  Find NCS groups from input model:        0.060
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
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      :  0.006   0.082   4250  Z= 0.395
  Angle     :  1.105  26.405   5839  Z= 0.819
  Chirality :  0.047   0.414    667
  Planarity :  0.006   0.079    780
  Dihedral  : 15.684  89.033   1382
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.06 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.81 (0.31), residues: 610
  helix: -0.24 (0.30), residues: 264
  sheet: -0.23 (1.38), residues: 17
  loop : -3.56 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 639 
 TYR   0.034   0.003   TYR A 691 
 PHE   0.014   0.002   PHE B 693 
 TRP   0.021   0.002   TRP A 752 
 HIS   0.009   0.002   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 4249)
  covalent geometry    : angle       1.10495 ( 5839)
  hydrogen bonds       : bond        0.13875 (  206)
  hydrogen bonds       : angle       7.29247 (  609)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: B  615 MET cc_start: 0.8472 (mmm) cc_final: 0.8215 (tpp)
REVERT: B  666 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6560 (tmmt)
REVERT: B  731 PHE cc_start: 0.7882 (t80) cc_final: 0.7256 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0595
  time to fit residues: 6.9522
Evaluate side-chains
  59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
B 633 ASN
A 757 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118085 restraints weight = 10715.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120429 restraints weight = 7575.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122180 restraints weight = 5821.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123368 restraints weight = 4735.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.124366 restraints weight = 4055.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   4250  Z= 0.284
  Angle     :  0.781   7.680   5839  Z= 0.430
  Chirality :  0.044   0.143    667
  Planarity :  0.006   0.055    780
  Dihedral  : 11.719  86.874    724
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.97 %
    Favored  : 88.03 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.45 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.71 (0.31), residues: 610
  helix: -0.33 (0.29), residues: 266
  sheet: -2.30 (1.02), residues: 27
  loop : -3.22 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 585 
 TYR   0.027   0.003   TYR B 605 
 PHE   0.032   0.003   PHE A 693 
 TRP   0.028   0.003   TRP A 752 
 HIS   0.008   0.003   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 4249)
  covalent geometry    : angle       0.78083 ( 5839)
  hydrogen bonds       : bond        0.05437 (  206)
  hydrogen bonds       : angle       6.34341 (  609)
  Misc. bond           : bond        0.00187 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: B  562 HIS cc_start: 0.8337 (m90) cc_final: 0.8097 (m90)
REVERT: B  581 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: A  530 ASN cc_start: 0.7335 (t0) cc_final: 0.7017 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0564
  time to fit residues: 5.5470
Evaluate side-chains
  58 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN
A 757 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.143084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.123279 restraints weight = 10409.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126224 restraints weight = 6975.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128313 restraints weight = 5147.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129834 restraints weight = 4062.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.130971 restraints weight = 3372.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4250  Z= 0.144
  Angle     :  0.620   6.151   5839  Z= 0.333
  Chirality :  0.040   0.146    667
  Planarity :  0.005   0.047    780
  Dihedral  : 11.166  76.898    724
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  5.32 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.33), residues: 610
  helix:  0.58 (0.31), residues: 269
  sheet: -2.28 (0.99), residues: 27
  loop : -2.77 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 585 
 TYR   0.024   0.002   TYR B 605 
 PHE   0.031   0.002   PHE A 707 
 TRP   0.025   0.003   TRP A 752 
 HIS   0.005   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4249)
  covalent geometry    : angle       0.61979 ( 5839)
  hydrogen bonds       : bond        0.04273 (  206)
  hydrogen bonds       : angle       5.34976 (  609)
  Misc. bond           : bond        0.00030 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: B  632 SER cc_start: 0.8693 (m) cc_final: 0.8397 (m)
REVERT: B  731 PHE cc_start: 0.7928 (t80) cc_final: 0.7289 (t80)
REVERT: A  530 ASN cc_start: 0.6951 (t0) cc_final: 0.6607 (t0)
REVERT: A  633 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8475 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0586
  time to fit residues: 6.4049
Evaluate side-chains
  64 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0970
   chunk 12 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 633 ASN
B 773 ASN
A 609 ASN
A 757 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.144747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126283 restraints weight = 10005.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128878 restraints weight = 6828.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130801 restraints weight = 5121.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132243 restraints weight = 4083.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133230 restraints weight = 3411.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4250  Z= 0.127
  Angle     :  0.596   6.044   5839  Z= 0.318
  Chirality :  0.041   0.147    667
  Planarity :  0.005   0.044    780
  Dihedral  : 10.772  84.590    724
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.34), residues: 610
  helix:  0.98 (0.32), residues: 270
  sheet: -2.10 (1.00), residues: 27
  loop : -2.58 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 770 
 TYR   0.019   0.002   TYR B 605 
 PHE   0.016   0.002   PHE A 693 
 TRP   0.022   0.002   TRP A 752 
 HIS   0.004   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4249)
  covalent geometry    : angle       0.59636 ( 5839)
  hydrogen bonds       : bond        0.03660 (  206)
  hydrogen bonds       : angle       4.81259 (  609)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B  585 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7978 (mmt90)
REVERT: A  530 ASN cc_start: 0.7274 (t0) cc_final: 0.6904 (t0)
REVERT: A  788 MET cc_start: 0.8357 (mmt) cc_final: 0.8096 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0653
  time to fit residues: 6.5721
Evaluate side-chains
  61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0970
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B 773 ASN
A 633 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.146353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127255 restraints weight = 10015.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129965 restraints weight = 6784.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.131979 restraints weight = 5053.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133330 restraints weight = 4006.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.134545 restraints weight = 3360.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4250  Z= 0.113
  Angle     :  0.571   6.083   5839  Z= 0.302
  Chirality :  0.039   0.147    667
  Planarity :  0.005   0.044    780
  Dihedral  : 10.299  87.248    724
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  4.26 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.34), residues: 610
  helix:  1.18 (0.32), residues: 272
  sheet: -1.89 (1.04), residues: 27
  loop : -2.45 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 585 
 TYR   0.023   0.002   TYR B 582 
 PHE   0.011   0.002   PHE B 566 
 TRP   0.016   0.002   TRP A 601 
 HIS   0.004   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 4249)
  covalent geometry    : angle       0.57140 ( 5839)
  hydrogen bonds       : bond        0.03289 (  206)
  hydrogen bonds       : angle       4.58032 (  609)
  Misc. bond           : bond        0.00028 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: B  581 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8285 (mt-10)
REVERT: B  731 PHE cc_start: 0.7884 (t80) cc_final: 0.7276 (t80)
REVERT: A  530 ASN cc_start: 0.6969 (t0) cc_final: 0.6602 (t0)
REVERT: A  788 MET cc_start: 0.8340 (mmt) cc_final: 0.8017 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0635
  time to fit residues: 6.3748
Evaluate side-chains
  57 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 633 ASN
B 773 ASN
B 790 GLN
A 757 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122445 restraints weight = 10606.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125160 restraints weight = 7268.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127180 restraints weight = 5460.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128537 restraints weight = 4347.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129736 restraints weight = 3650.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4250  Z= 0.175
  Angle     :  0.625   6.173   5839  Z= 0.337
  Chirality :  0.041   0.136    667
  Planarity :  0.005   0.045    780
  Dihedral  : 10.208  79.491    724
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.34), residues: 610
  helix:  0.91 (0.31), residues: 270
  sheet: -1.63 (1.05), residues: 28
  loop : -2.54 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 604 
 TYR   0.014   0.002   TYR B 605 
 PHE   0.017   0.002   PHE A 762 
 TRP   0.011   0.002   TRP A 601 
 HIS   0.004   0.002   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4249)
  covalent geometry    : angle       0.62505 ( 5839)
  hydrogen bonds       : bond        0.03806 (  206)
  hydrogen bonds       : angle       4.90513 (  609)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7562 (t0) cc_final: 0.7199 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0599
  time to fit residues: 5.5996
Evaluate side-chains
  57 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 773 ASN
A 633 ASN
A 757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.143594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.123896 restraints weight = 10446.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126635 restraints weight = 7209.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128652 restraints weight = 5433.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130164 restraints weight = 4347.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131334 restraints weight = 3645.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4250  Z= 0.130
  Angle     :  0.583   6.069   5839  Z= 0.309
  Chirality :  0.040   0.147    667
  Planarity :  0.005   0.045    780
  Dihedral  :  9.931  75.943    724
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.34), residues: 610
  helix:  1.16 (0.31), residues: 272
  sheet: -2.65 (0.70), residues: 52
  loop : -2.61 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 585 
 TYR   0.014   0.002   TYR B 605 
 PHE   0.019   0.002   PHE A 693 
 TRP   0.014   0.002   TRP A 752 
 HIS   0.003   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4249)
  covalent geometry    : angle       0.58324 ( 5839)
  hydrogen bonds       : bond        0.03341 (  206)
  hydrogen bonds       : angle       4.59735 (  609)
  Misc. bond           : bond        0.00029 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: B  582 TYR cc_start: 0.9202 (t80) cc_final: 0.8924 (t80)
REVERT: A  530 ASN cc_start: 0.7358 (t0) cc_final: 0.6997 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0502
  time to fit residues: 4.8328
Evaluate side-chains
  55 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0020
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.2966

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

Flipped N/Q/H residues before XYZ refinement:
B 773 ASN
A 633 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.128930 restraints weight = 10156.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131597 restraints weight = 7081.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.133592 restraints weight = 5341.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.135093 restraints weight = 4285.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136223 restraints weight = 3587.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4250  Z= 0.108
  Angle     :  0.579   5.968   5839  Z= 0.303
  Chirality :  0.040   0.152    667
  Planarity :  0.005   0.045    780
  Dihedral  :  9.482  70.970    724
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.71 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.35), residues: 610
  helix:  1.41 (0.32), residues: 272
  sheet: -2.03 (0.81), residues: 42
  loop : -2.49 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 585 
 TYR   0.038   0.002   TYR A 605 
 PHE   0.012   0.001   PHE B 566 
 TRP   0.018   0.002   TRP A 752 
 HIS   0.003   0.001   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4249)
  covalent geometry    : angle       0.57879 ( 5839)
  hydrogen bonds       : bond        0.02996 (  206)
  hydrogen bonds       : angle       4.17403 (  609)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7276 (t0) cc_final: 0.6878 (t0)
REVERT: A  592 LEU cc_start: 0.4125 (tp) cc_final: 0.3876 (tp)
REVERT: A  650 GLU cc_start: 0.8472 (pt0) cc_final: 0.8257 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0505
  time to fit residues: 5.0016
Evaluate side-chains
  60 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0010
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.143272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.123932 restraints weight = 10398.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.126506 restraints weight = 7252.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128433 restraints weight = 5529.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.129857 restraints weight = 4454.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.130960 restraints weight = 3760.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4250  Z= 0.147
  Angle     :  0.603   6.152   5839  Z= 0.320
  Chirality :  0.040   0.138    667
  Planarity :  0.005   0.046    780
  Dihedral  :  9.254  63.848    724
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.77 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.35), residues: 610
  helix:  1.33 (0.32), residues: 272
  sheet: -2.45 (0.72), residues: 52
  loop : -2.51 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 604 
 TYR   0.016   0.002   TYR A 605 
 PHE   0.022   0.002   PHE A 693 
 TRP   0.036   0.003   TRP A 752 
 HIS   0.003   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4249)
  covalent geometry    : angle       0.60332 ( 5839)
  hydrogen bonds       : bond        0.03391 (  206)
  hydrogen bonds       : angle       4.46608 (  609)
  Misc. bond           : bond        0.00028 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: B  582 TYR cc_start: 0.8953 (t80) cc_final: 0.8635 (t80)
REVERT: A  530 ASN cc_start: 0.7336 (t0) cc_final: 0.6998 (t0)
REVERT: A  633 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8200 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0486
  time to fit residues: 4.6230
Evaluate side-chains
  56 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0980
   chunk 8 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0170
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.4224

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

Flipped N/Q/H residues before XYZ refinement:
A 708 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.143201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.124474 restraints weight = 10109.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126988 restraints weight = 7001.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128910 restraints weight = 5329.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130316 restraints weight = 4295.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.131269 restraints weight = 3618.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4250  Z= 0.169
  Angle     :  0.634   6.101   5839  Z= 0.337
  Chirality :  0.041   0.140    667
  Planarity :  0.005   0.045    780
  Dihedral  :  9.143  59.003    724
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.35), residues: 610
  helix:  1.16 (0.32), residues: 269
  sheet: -2.54 (0.71), residues: 52
  loop : -2.55 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 787 
 TYR   0.041   0.002   TYR A 605 
 PHE   0.013   0.002   PHE B 640 
 TRP   0.031   0.003   TRP A 752 
 HIS   0.004   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4249)
  covalent geometry    : angle       0.63400 ( 5839)
  hydrogen bonds       : bond        0.03519 (  206)
  hydrogen bonds       : angle       4.62123 (  609)
  Misc. bond           : bond        0.00027 (    1)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7536 (t0) cc_final: 0.7179 (t0)
REVERT: A  650 GLU cc_start: 0.8491 (pt0) cc_final: 0.8192 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0468
  time to fit residues: 4.2833
Evaluate side-chains
  54 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN
A 708 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.145046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125918 restraints weight = 10165.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128543 restraints weight = 7105.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130509 restraints weight = 5391.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.131969 restraints weight = 4329.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.133063 restraints weight = 3644.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4250  Z= 0.119
  Angle     :  0.603   8.785   5839  Z= 0.312
  Chirality :  0.040   0.148    667
  Planarity :  0.005   0.045    780
  Dihedral  :  8.743  58.358    724
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.35 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.35), residues: 610
  helix:  1.38 (0.32), residues: 269
  sheet: -2.03 (0.81), residues: 42
  loop : -2.47 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 787 
 TYR   0.014   0.002   TYR A 605 
 PHE   0.021   0.002   PHE A 693 
 TRP   0.036   0.003   TRP A 752 
 HIS   0.003   0.001   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4249)
  covalent geometry    : angle       0.60257 ( 5839)
  hydrogen bonds       : bond        0.03139 (  206)
  hydrogen bonds       : angle       4.29874 (  609)
  Misc. bond           : bond        0.00022 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 858.76 seconds
wall clock time: 15 minutes 26.71 seconds (926.71 seconds total)